Skip to main content

Table 2 Ensembl gene model corrections (A) and novel additions (B) to Ensembl Genebuild (e70)

From: Genomics analysis of potassium channel genes in songbirds reveals molecular specializations of brain circuits for the maintenance and production of learned vocalizations

Revised HUGO term

Ensembl model or chromosome location

Current ensembl annotation (taegut3.2.4 )

Implication for zebra finch genome

Explanation

2A - Corrections

KCNA6

ENSTGUG00000011959

Novel Pseudogene

KCNA6 is present

Model truncated due to gaps in genomic sequence

KCNAB1

ENSTGUG00000011253; ENSTGUG00000011240

Novel Gene

KCNAB1 is present

ENSTGUG00000011253, which corresponds to the 3′ part of the gene, is incorrectly placed upstream of ENSTGUG00000011240, which represents the 5′ part of the same gene

KCNAB2 allele$

ENSTGUG00000013969

Novel Gene

KCNAB2 has an allele.

Model maps to Chr Unknown and has high sequence identity to KCNAB2, so it is likely an allele

KCNB2

ENSTGUG00000011511

Novel Pseudogene

KCNB2 is present

Model truncated due to gaps in genomic sequence

KCND2

ENSTGUG00000004681

Novel Gene

KCND2 is present

ENSTGUG00000004681 and ENSTGUG00000004691 (Table 1) are different parts of KCND2.

KCTD4

ENSTGUG00000018368

B5FX54_TAEGU

KCTD4 is present

Model truncated due to gaps in genomic sequence

KCTD4 allele$

ENSTGUG00000018204

B5FX54_TAEGU

KCTD4 is present (ENSTGUG00000018368; see above) but not duplicated

Model maps to Chr Unknown and has high sequence identity to KCTD4, so it is likely an allele

KCNJ3

ENSTGUG00000012153

Novel Gene

KCNJ3 is present; KCNJ3L is a duplication of KCNJ3.

Model not annotated

KCNJ3L

ENSTGUG00000002970

KCNJ3

Duplication of KCNJ3 (ENSTGUG00000012153), absent in humans

See results text

KCNJ12

ENSTGUG00000007541

Novel Pseudogene

KCNJ12 is present

Model truncated due to gaps in genomic sequence

KCNK16L

ENSTGUG00000013021

Novel Gene

Duplication of KCNK16 (no model), absent in humans.

See results text

KCNQ1L

ENSTGUG00000012696

Novel Gene

Duplication of KCNQ1 (ENSTGUG00000009167), absent in mammals

Model not annotated

KCNQ4

ENSTGUG00000017337

Novel Gene

KCNQ4 is present

Model not annotated

KCNS2

ENSTGUG00000012021

Novel Pseudogene

KCNS2 is present

Model truncated due to gaps in genomic sequence

KCNV2L

ENSTGUG00000000100

Novel Gene

Duplication of KCNV2 (ENSTGUG00000005377), absent in humans

See results text

KCTD12L

ENSTGUG00000005525

Novel Gene

Duplication of KCTD12 (ENSTGUG00000008750); absent in humans

See results text

2B - Additions

KCNE1P

Chr1B_rand:70101-70314

None

Pseudogene duplication of KCNE1 (ENSTGUG00000016311), unique to zebra finch

Gene truncated but no gaps, high quality sequence

KCNJ5/9 L

Chr24:252787-253805

None

KCNJ5 or KCNJ9 duplicated, but absent in humans

Gene truncated due to gaps in genomic sequence

KCNK16

Chr3:29820700-29833238

None

KCNK16 is present

Gene truncated due to gaps in genomic sequence

KCTD18

Chr7:22280633-22353729

None

KCTD18 is present

Gene truncated due to gaps in genomic sequence

  1. $ - These corrected models represent putative alleles and are therefore not included in Table 1.