RetrogeneDB ID: retro_ggal_22

Retrocopy location

• Organism: Chicken (Gallus gallus)
• Coordinates: W:626747..627211(+)
• Located in intron of: ENSGALG00000014441

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINS2
• Ensembl ID: ENSGALG00000028131
• Aliases: None
• Description: GINS complex subunit 2 (Psf2 homolog) [Source:HGNC Symbol;Acc:24575]

Sequence

>retro_ggal_22
GGGGATCTGGGTCCTTTCAACCCTGGTTTGCTGGTGGAAGTGCCTGTCTGGTTGGCCATCAATCTGAAGCAGAGGTAGAA
ATGCCACCTGATTCCCCTGGAGTGGATGGACATAGAAAAACTGGAGAAAATTTGGGACCAGGAATACACCAGGACACCTT
CACTCCCATGCCTAGTCTCTGTTATGTGGAATTCACAAAGCTGCTCTTAAACTACACCTCAAATAACATCCCCAAAGCTG
TCAAGATTCAAATGTTGGTGAAGGATACATGGGACACACGGATGGCCAAGCTGCGGCTGTCTGCAGACAGCTTCATCTGG
AAACAGGAGGCCCATGCCAAGCTGGATAATCTAATGTTGATGGAGATCAACACCATTGGGATTTTCCTTACTCGAGCCTT
AGATCACATGTACAAACTCTGGACTAACCTCCAGCCTGACAGGAGCGTCAAGTTCCAGGATTTC

Alignment

ORF - retro_ggal_22 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.21 %
• Parental protein coverage: 83.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GDLGPFNPGLPVEVPVWLAINLKQRQKCRLIPPAWMDVEKLEEIRDQERK-EDTFTPMPSPYYMELTKLL
          GDLGPFNPGL.VEVPVWLAINLKQR.KC.LIP..WMD.EKLE.I.DQE....DTFTPMPS..Y.E.TKLL
Retrocopy GDLGPFNPGLLVEVPVWLAINLKQR*KCHLIPLEWMDIEKLEKIWDQEYT<QDTFTPMPSLCYVEFTKLL

Parental  LNYASDNIPKADEIRTLVKDTWDTRMAKLRLSADSFVRQQEAHAKLDNLTLMEINTIGTFLTQALDHMYK
          LNY.S.NIPKA..I..LVKDTWDTRMAKLRLSADSF...QEAHAKLDNL.LMEINTIG.FLT.ALDHMYK
Retrocopy LNYTSNNIPKAVKIQMLVKDTWDTRMAKLRLSADSFIWKQEAHAKLDNLMLMEINTIGIFLTRALDHMYK

Parental  LRTNLQPSGSAESQDF
          L.TNLQP..S...QDF
Retrocopy LWTNLQPDRSVKFQDF

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	0.06 RPM	1.20 RPM
SRP007412_cerebellum	0.00 RPM	1.01 RPM
SRP007412_heart	0.05 RPM	0.20 RPM
SRP007412_kidney	0.12 RPM	0.81 RPM
SRP007412_liver	0.06 RPM	0.34 RPM
SRP007412_testis	0.00 RPM	19.03 RPM

ChIP-Seq

Gallus gallus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ggal_22 retrocopy.

TSS

Gallus gallus was not studied using FANTOM5 data.

Lab

retro_ggal_22 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggal_22 has 0 orthologous retrocopies within neognath group .

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Parental genes homology:

Parental genes homology involve 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000017303	1 retrocopy	retro_cjac_3309,
Dasypus novemcinctus	ENSDNOG00000008760	4 retrocopies	retro_dnov_1034, retro_dnov_166, retro_dnov_2424, retro_dnov_604,
Homo sapiens	ENSG00000131153	1 retrocopy	retro_hsap_2477,
Gallus gallus	ENSGALG00000028131	1 retrocopy	retro_ggal_22 ,
Gorilla gorilla	ENSGGOG00000009069	2 retrocopies	retro_ggor_1542, retro_ggor_960,
Macropus eugenii	ENSMEUG00000014703	1 retrocopy	retro_meug_1479,
Microcebus murinus	ENSMICG00000016691	1 retrocopy	retro_mmur_342,
Macaca mulatta	ENSMMUG00000020594	1 retrocopy	retro_mmul_596,
Pongo abelii	ENSPPYG00000007616	2 retrocopies	retro_pabe_1826, retro_pabe_896,
Pan troglodytes	ENSPTRG00000008430	1 retrocopy	retro_ptro_1433,
Pteropus vampyrus	ENSPVAG00000004944	1 retrocopy	retro_pvam_762,
Sarcophilus harrisii	ENSSHAG00000015249	1 retrocopy	retro_shar_382,
Sus scrofa	ENSSSCG00000002663	1 retrocopy	retro_sscr_883,
Tupaia belangeri	ENSTBEG00000006220	1 retrocopy	retro_tbel_1328,