RetrogeneDB ID: retro_ggor_2027

Retrocopy location

• Organism: Gorilla (Gorilla gorilla)
• Coordinates: 4:42463325..42463928(+)
• Located in intron of: ENSGGOG00000001861

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATP1B1
• Ensembl ID: ENSGGOG00000002499
• Aliases: None
• Description: None

Sequence

>retro_ggor_2027
CCACCAGGATTAACACAGATTTCTCAGATCCAGCAGACTGAAATTGCCTTTCATCCTAATGATCCCAAGCACTGTGAGGC
ATATGTGCTGAACGTAGTTAGGTTCCTGGAAAAGTACAAAGATTCAGCCCAGAAGGATGACATGATTTTTGAAAATTGTG
ACAATGTGCCCAGTGAACCCAAAGAACAAGGAGACTTTAATCAAGAATGAGGTGAGCGAAAGGTCTGCAGATTCAAGCTT
GAGTGGCTGGGAAATTGCTCTGGATTAAATGACAAAACTTACGGCTACGAAGAAGGCAAACCACATGTTATTATAAAGCT
CAAGTGAGTTCTAGGCTTCAAACCTAAGTCTCCCGAGAATGAGTCCTTGGAGACTTACCCAGTGATGAAGTATAACGCAT
CTGTCTTTCCTGTTCAGTGCACTGGCTAGCGAGATGAAGATAAGGATAAAAATAGAAATGTGGAGTATTTTGGACTGGGC
ACCTACCTTGGTTTTCCTCTGCAGAATTATCCCTACTATGGCAAACTCCTGCAGCCCAAATACCTGCAGCCCCTGCTTGC
TGTACAGTTCACCAACCTTACCATGGACACTGAAATTCGCCTA

Alignment

ORF - retro_ggor_2027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.08 %
• Parental protein coverage: 66.34 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PPGLTQIPQIQKTEISFRPNDPKSYEAYVLNIVRFLEKYKDSAQRDDMIFEDCGDMPSEPKERGDFNHER
          PPGLTQI.QIQ.TEI.F.PNDPK..EAYVLN.VRFLEKYKDSAQ.DDMIFE.C...PSEPKE.GDFN.E.
Retrocopy PPGLTQISQIQQTEIAFHPNDPKHCEAYVLNVVRFLEKYKDSAQKDDMIFENCDNVPSEPKEQGDFNQE*

Parental  GERKVCRFKLEWLGNCSGLNDETYGYKEGKPCIIIKLNRVLGFKPKPPKNESLETYPVMKYNPNVLPVQC
          GERKVCRFKLEWLGNCSGLND.TYGY.EGKP..IIKL..VLGFKPK.P.NESLETYPVMKYN..V.PVQC
Retrocopy GERKVCRFKLEWLGNCSGLNDKTYGYEEGKPHVIIKLK*VLGFKPKSPENESLETYPVMKYNASVFPVQC

Parental  TGKRDEDKDKVGNVEYFGLGNSPGFPLQYYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRI
          TG.RDEDKDK..NVEYFGLG...GFPLQ.YPYYGKLLQPKYLQPLLAVQFTNLTMDTEIR.
Retrocopy TG*RDEDKDKNRNVEYFGLGTYLGFPLQNYPYYGKLLQPKYLQPLLAVQFTNLTMDTEIRL

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_prefrontal_cortex	0.14 RPM	759.88 RPM
SRP007412_cerebellum	0.32 RPM	289.26 RPM
SRP007412_heart	0.00 RPM	56.41 RPM
SRP007412_kidney	0.20 RPM	1083.06 RPM
SRP007412_liver	0.24 RPM	77.05 RPM
SRP007412_testis	0.10 RPM	73.14 RPM

ChIP-Seq

Gorilla gorilla was not studied using ChIP-Seq data.

EST

Gorilla gorilla was not studied using EST data.

TSS

Gorilla gorilla was not studied using FANTOM5 data.

Lab

retro_ggor_2027 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ggor_2027 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2924
Pan troglodytes	retro_ptro_1979
Callithrix jacchus	retro_cjac_2288

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000010317	1 retrocopy	retro_cjac_2288,
Homo sapiens	ENSG00000143153	1 retrocopy	retro_hsap_2924,
Gorilla gorilla	ENSGGOG00000002499	1 retrocopy	retro_ggor_2027 ,
Pan troglodytes	ENSPTRG00000001653	1 retrocopy	retro_ptro_1979,
Xiphophorus maculatus	ENSXMAG00000016407	1 retrocopy	retro_xmac_22,