RetrogeneDB ID: retro_ggal_18

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: 4:9043455..9043944(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: POUV
• Ensembl ID: ENSGALG00000026574
• Aliases: POUV, OCT4
• Description: POU domain class 5 transcription factor 1 [Source:RefSeq peptide;Acc:NP_001103648]

Sequence

>retro_ggal_18
GAGGACACGCCGACCTCGGACGACCTGGAGCAGTTCGCCAAGCAGTTCAAGCAGCGGCGGATTAAGCTGGGCTTCACGCA
GGCCGACGTGGGGCTGGCGCTGGGCACCCTGTACGGCAACGTCTTCTCGCAGACCACCATCTGCCGCTTCGAGGCCCTGC
AGCTCAGCTTCAAGAACATGTGCAAGCTGAAGCCGCTGCTGAACAAGTGGCTGGAGGAGGCCGACTCCTCCACCGGCAGC
CCCACCAGCATCGACAAGATCGCGGCGCAGGGCAGGAAGAGGAAGAAGCGCACCTCCATCGAGGTGAGTGTCAAAGGCGT
GCTGGAGACGCACTTCCTCAAGTGCCCCAAGCCGGCCGCGCAGGAGATCTCCTCGCTGGCGGACAGCCTGCAGCTGGAGA
AGGAGGTGGTGCGGGTCTGGTTCTGCAACCGGCGGCAGAAGGAGAAGCGCATGACGCCGCCGGGCGAGCAGCAGCAGCAC
GAGGTGTAC

Alignment

ORF - retro_ggal_18 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.86 %
• Parental protein coverage: 56.27 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QDAPTSEELEQFAKDLKHKRIMLGFTQADVGLALGTLYGKMFSQTTICRFEALQLSFKNMCKLKPLLQRW
          .D.PTS..LEQFAK..K..RI.LGFTQADVGLALGTLYG..FSQTTICRFEALQLSFKNMCKLKPLL..W
Retrocopy EDTPTSDDLEQFAKQFKQRRIKLGFTQADVGLALGTLYGNVFSQTTICRFEALQLSFKNMCKLKPLLNKW

Parental  LNEAENTDNMQEMCNAEQVLAQARKRKRRTSIETNVKGTLESFFRKCVKPSPQEISQIAEDLNLDKDVVR
          L.EA................AQ.RKRK.RTSIE..VKG.LE..F.KC.KP..QEIS..A..L.L.K.VVR
Retrocopy LEEADSSTG--SPTSIDKIAAQGRKRKKRTSIEVSVKGVLETHFLKCPKPAAQEISSLADSLQLEKEVVR

Parental  VWFCNRRQKGKRLLLPFGNESEGVMY
          VWFCNRRQK.KR...P.G.......Y
Retrocopy VWFCNRRQKEKRMTPP-GEQQQHEVY

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP007412_brain	21.80 RPM	0.06 RPM
SRP007412_cerebellum	8.59 RPM	0.00 RPM
SRP007412_heart	0.20 RPM	0.05 RPM
SRP007412_kidney	10.41 RPM	0.00 RPM
SRP007412_liver	0.22 RPM	0.00 RPM
SRP007412_testis	2.37 RPM	3.17 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_18 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_18 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_18 has 1 orthologous retrocopies within neognath group .

Species	RetrogeneDB ID
Taeniopygia guttata	retro_tgut_25

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010377	3 retrocopies	retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus	ENSBTAG00000021111	2 retrocopies	retro_btau_1576, retro_btau_951,
Callithrix jacchus	ENSCJAG00000019789	1 retrocopy	retro_cjac_123,
Dipodomys ordii	ENSDORG00000009549	1 retrocopy	retro_dord_65,
Gallus gallus	ENSGALG00000026574	1 retrocopy	retro_ggal_18 ,
Meleagris gallopavo	ENSMGAG00000000739	1 retrocopy	retro_mgal_8,
Mustela putorius furo	ENSMPUG00000001202	2 retrocopies	retro_mputfur_253, retro_mputfur_96,
Mus musculus	ENSMUSG00000024406	2 retrocopies	retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus	ENSOCUG00000017160	3 retrocopies	retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Ictidomys tridecemlineatus	ENSSTOG00000026103	3 retrocopies	retro_itri_1076, retro_itri_1705, retro_itri_951,
Taeniopygia guttata	ENSTGUG00000002412	1 retrocopy	retro_tgut_25,