Discovery and characterization of 91 novel transcripts expressed in cattle placenta

Kumar, Charu G; Larson, Joshua H; Band, Mark R; Lewin, Harris A

doi:10.1186/1471-2164-8-113

BMC Genomics

Table 3 Sample feature table for 91 NTs

From: Discovery and characterization of 91 novel transcripts expressed in cattle placenta

NT Id^a	GenBank accession^b	length (bp)	ORF_length aa^c	species^d	No. exons	poly A signal^e	motif^f	tissue preference	Hg17 locus	BTAU_2.0 assignment	Cattle genome context^g	Segmental location^h
BTC1_14FL (XM_873204)	CK394134	868	63		4	AATAAA	CpG	muscle	7p13	chr4:43, 188,679–43,191, 770	intergenic	interstitial
BTC1_15FL	AY563860	630	none	C	1	AATAAA	ncRNA	none	14q11.2	scaffold3389:59,086–59,711	inter genie	interstitial
BTC1_33FL	CK394175	691	35	C	5	ATTAAA	CpG	none	6q14.3	scaffold4626:20,602–22,398	intergenic	interstitial
BTC1_34FL	CK394179	977	100 K	A	3	AATAAA	ADH_DRE, GY-Box, signalP	placentome	9q32	scaffold9964:10,570–17,798	intergenic	interstitial
BTC1_53FL	AY563751	525	106	C	1	AATAAA	none	none	19q13.31	chr6:49, 142,506–49,143,026	intergenic	interstitial
BTC1_55FL	AY563756	777	82 K	A	2	AATAGA	signalP	none	16q22.1	chr18:13,861,852–13,862,619	intergenic	boundary
BTC1_57FL	AY563869	911	none	C	1	AATAAA	none	thymus	7p22.1	chr25:33,360,786–33,361,318	ZnF447	interstitial
BTC1_58FL	AY563762	1544	64	A	2	ATTAAA	ADH_DRE, GY-Box	none	11q12.2	chr29:31,601,481–31,607,081	RAB3	interstitial
BTC1_71FL	AY563803	691	none	C	1	AATAAA		none	3p21.31	chr22:42,680,522–42,681,188	SACMIL	interstitial
BTC1_77FL	AY563824	1095	84	C	1	AATAAA	GY-Box; CpG	thymus	18q21.33	chr24:44,739,526–44,740,613	HDGFRP2	subtelomeric
BTC1_78FL	CK394028	1736	91 K	A	1	AATAAA	GY-Box; IR	mesenteric lymphnode, thymus	1p36.13	chr2:85,996,428–85,997,304	intergenic	subtelomeric
BTC1_79FL	AY563826	732	none	C	4	TATAAA	CpG; ncRNA	cerebrum	2p11.2	chr11:34,570,339–34,575,174	intergenic	interstitial
BTC1_92FL (XM_587188)	CK394038	933	93 K; 127	C	1	TGTAAA	none	cerebrum	17q25.1	chr19:49,709,796–49,710,719	intergenic	interstitial
BTC1_93FL	AY563890	1269	147 K	C	1	AATAAA	GY-Box	thymus	22q12.2	chr17:42,667,501–42,668,530	SEC14L4	interstitial
BTC1_95FL	AY563713	2492	108	C	1	AATAAA	none	skin	6p21.2	chr23:8,629,884–8,632,373	intergenic	interstitial
BTC1_102FL	AY563714	795	38 K	C	1	AATAAA	G-quartet; IR	none	10q11.21	chr28:33,147,612–33,148,436	intergenic	subtelomeric
BTC1_113FL (XM_611248)	CK394057	659	69 K	C	5	AATAAA	CpG	thalamus	1p35.3	chr2:76,776,847–76,779,658	intergenic	interstitial
BTC1_115FL	CK394060	962	36; 35	C	1	AATAAA	none	thymus	1p34.1	chr3:67,576,355–67,577,638	LRRC41	interstitial
BTC1_130FL (XM_611254)	CK394181	664	125 K; 65 K	A	3	AATAAA	none	adrenal, cerebellum, thalamus	19q13.43	chr18:55591568–55593819	ZIM2	subtelomeric
BTC1_132FL	CK394199	2174	none	A	1	AATAAA	IR; ncRNA	thymus	Xq25	scaffold4717:48,263–50,399	ERVK6	interstitial
BTC3_7JE	CK393999	548	35	A	5	AATAAA	none	muscle	7p22.1	chr4:43,188,676–43,191,750	intergenic	interstitial
BTC1_22JE	CK394011	1569	none	A	1	ATTAAA	IR; ncRNA	placentome	5q33.3	scaffold399:92,975–94,544	TIMD4	interstitial
BTC2_43JE	CK394035	1043	none	C	2	AAACAA	G-quartet; CpG	cerebrum, thalamus	8q24.3	scaffold12671:9,483–10,533	JRK	interstitial
BTC1_51JE	CK394043	958	130	C	2	AATAAA	none	skin	11p15.5	scaffold2079:18,521–19,645	intergenic	interstitial
BTC1_100JE	CK394097	2381	92 K	C	1	GATAAA	GY-Box	none	19p13.11	chr7:5,772,691–5,775,068	intergenic	interstitial
BTC1_104JE (XM_883284)	CK394101	619	59; 68	A	5	AATAAA	None	placentome	none	scaffold6598:22994–33093	intergenic	interstitial
BTC1_113JE	CK394107	830	none	A	2	AATAAA	CpG; ncRNA	none	1p13.2	scaffold1237:214289–215207	intergenici	interstitial
BTC1_118JE	CK394113	2257	50; 92	C	1	AATAAA	GY-Box	none	22q13.2	scaffold9684:8273–9215	intergenic	interstitial
BTC1_144JE	CK394138	832	150 K	C	1	AATAAA	none	none	1p36.33	chr16:37642343–37643174	intergenic	boundary
BTC1_146JE	CK394139	2206	none	A	3	ATTAAA	IR; ncRNA	muscle, skin	14q32.31	chr21:45,674,164–45,678,931	intergenic	interstitial
BTC1_203JE	CK394182	773	129 K	C	3	ATTAAA	CpG	heart	8q21.2	chr14:46,885,318–46,890,350	intergenic	interstitial
BTC1_215JE	CK394201	1038	109 K	C	1	AATAAA	Eu_thiol protease	none	2p25.3	scaffold473:40,328–41,349	intergenic	interstitial
BTC1_8NG	AY563705	703	71 K	A	4	AATATA	none	thalamus	none	chr19:48,755,357–48,757,924	ATP1a2a	interstitial
BTC1_39NG	AY563711	767	172 K	C	2	AATAAA	Proline-rich with_coiled-coil	none	1p31.3	scaffold997:257,434–259,042	INADL	interstitial
BTC1_58NG	AY563715	562	49	C	1	AATAAA	CpG	cerebrum	13q34	chr12:48,063,584–48,064,091	CDC16:	subtelomeric
BTC1_63NG	AY563716	483	142 K	C	2	unknown	signalP; ATPaseE1. E2	none	16p13.12	chr25:14,893,445–14,897,173	intergenic	interstitial
BTC1_104NG	AY563722	728	144 K; 149 K	C	1	AATAAA	TOP	none	14q32.32	chr21:48,386,644–48,387,349	MKNK2 i	subtelomeric
BTC1_149NG	AY563726	690	35	C	1	TATAAA	CpG	skin, testis	22q11.21	chr17:45,366,139–45,366,804	RFNG	subtelomeric
BTC1_237NG	AY563754	622	67	C	1	AATAAA	CpG	cerebrum	17q25.3	chr19:47,237,560–47,238,117	intergenic	interstitial
BTC1_255NG (XM_596632)	AY563763	651	64	C	2	AATAAA	CpG;Heavy metal_ion transport	muscle	3q29	chr1:43,207,885–43,208,506	intergenic	interstitial
BTC1_269NG	AY563771	716	116	C	1	ATTAAA	CpG	none	11q13.3	chr29:41,407,248–41,407,965	intergenic	boundary
BTC1_286NG (XM_870778)	AY563780	788	36; 184 K	C	1	unknown	CpG	placentome	none	chr14:662,313–663,087	MAPK8IP2	subtelomeric

^a number in parenthesis is the GenBank accession of the cattle RefSeq prediction matching the NT.
^b GenBank accession No. of 3' sequence including primer-walked sequence.
^c K denotes start-codon of ORF flanked by Kozak consensus.
^dC, cattle-specific; A, cetartiodactyla-specific
^e 'Unknown' indicates that a polyadenylation signal could not be identified.
^f 'IR' indicates presence of an inverse repeat; ADH_DRE, GY-box, K-box, Brd box and CPE are functional UTR elements.
gene symbol indicates NT is located in an intron of that gene.
^h "Boundary" indicates that the NT anchors within 1 Mbp of the end of a homologous synteny boundary on a human chromosome as defined in [23];
"Subtelomeric" indicates that the NT aligns within 2 Mbp from the end of a cattle chromosome.

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ISSN: 1471-2164

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