RetrogeneDB ID: retro_pabe_3084

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 7:103797370..103798195(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C10orf26
• Ensembl ID: ENSPPYG00000002610
• Aliases: None
• Description: None

Sequence

>retro_pabe_3084
AGAAGGCTCCTAGGTGGCGTGGCACTCCTGCTTCTCCCAGCGATGCCCAGCCCCCTGTCAGTGAGGGCTGAACCCCCACA
GGATAAGGAAGCCTGAGTGAATACCAATAATCAAAGCTACATCTGTGACACAGGACACTGCTGTGGACAGTATCAGTGCT
GCAACTACTGCTAGGAACTCTGGTGGCTCTGGCTGGTGTGGACCATCATCATCATCCTTAGCTGCTGCTACATTGGCCAC
CACCGCCAAGCCAAGCACCGCCTTCAGGCCCAGCATGGGCAACATGAAATCAACCTGATCCCCTGCCGAGAAGCCTTCAA
TCACTCAGTGCTGCCCTTTTTATTTTCAGGTTTTTACTAAACTACTTTAACTACCTCCCTTATGAGGAAGTGGTGAGCCC
AGCCCTCCAACTCCCTCCTCCAGCATACAGTGCCTTTCCAGCTACACAGCAGCAGCAGCTCCTGCCTCCACAGTGCGGCC
TGGCAGGTGGCAGTCCCCCGGCGCCAATCCCACCAGGGGATCCAAGGGAATCCCTTGTCTGAGCCCAGCAGAAGCATCAC
AAGACCCCCAAGCATCGCTGATCCTGAGCCCTCTGACCTACCAGGTGACCGAGTAGCCACCAAAGCCCTAGGGATGCAGC
CCAGTGGCTCTGTAGCCAGCCTGGGAGAGCTGGACCCAGGGGCCTTCCTGGACAAGGATGCAGAATGTAAGGAGGAGCTG
CTGAAAGATGACAGTTCTGAACATGGCAGCGCACCACCGACAGACAGCAAAGAGAAGATGCTCAGGAGACATCACCGCTT
CACTGGTGACTCGGGCATTGAAGTG

Alignment

ORF - retro_pabe_3084 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.47 %
• Parental protein coverage: 74.93 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  RRLLGGMALLLLQALPSPLSARAEPPQDKEACVGTNNQSYICDTGHCCGQSQCCNYYYELWWFWLVWTII
          RRLLGG.ALLLL.A.PSPLS.RAEPPQDKEA.V.TNNQSYICDTGHCCGQ.QCCNY..ELWW.WLVWTII
Retrocopy RRLLGGVALLLLPAMPSPLSVRAEPPQDKEA*VNTNNQSYICDTGHCCGQYQCCNYC*ELWWLWLVWTII

Parental  IILSCCCVCHHRRAKHRLQAQQRQHEINLIAYREAHNYSAL-PFYFRFLPNYL-LPP-YEEVVNRP-PTP
          IILSCC...HHR.AKHRLQAQ..QHEINLI..REA.N.S.L.PFYF......L.LPP.YEEVV......P
Retrocopy IILSCCYIGHHRQAKHRLQAQHGQHEINLIPCREAFNHSVL>PFYFQVFTKLL*LPP>YEEVVSPALQLP

Parental  PPPYSAF-QLQQQQLLPPQCGPAGGSP-PGVDPTRGSQGAQSSPLSGPSRSS-TRPPSIADPEPSDLPVE
          PP.YSAF...QQQQLLPPQCG.AGGSP.PG..PTRGS.G....P...P...S.TRPPSIADPEPSDLP..
Retrocopy PPAYSAFPATQQQQLLPPQCGLAGGSP<PGANPTRGSKGI---PCLSPAEAS<TRPPSIADPEPSDLPGD

Parental  RAATKAPGMEPSGSVAGLGELDPGAFLDKDAECREELLKDDSSEHGA---PDSKEKTPGRHRRFTGDSGI
          R.ATKA.GM.PSGSVA.LGELDPGAFLDKDAEC.EELLKDDSSEHG.....DSKEK...RH.RFTGDSGI
Retrocopy RVATKALGMQPSGSVASLGELDPGAFLDKDAECKEELLKDDSSEHGSAPPTDSKEKMLRRHHRFTGDSGI

Parental  EV
          EV
Retrocopy EV

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	0.17 RPM	33.28 RPM
SRP007412_cerebellum	0.12 RPM	27.85 RPM
SRP007412_heart	0.06 RPM	18.00 RPM
SRP007412_kidney	0.10 RPM	61.65 RPM
SRP007412_liver	0.00 RPM	34.30 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_3084 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_3084 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_3084 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3774
Macaca mulatta	retro_mmul_1640

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014336	1 retrocopy	retro_btau_855,
Choloepus hoffmanni	ENSCHOG00000007532	1 retrocopy	retro_chof_1174,
Callithrix jacchus	ENSCJAG00000018079	1 retrocopy	retro_cjac_2235,
Homo sapiens	ENSG00000166272	1 retrocopy	retro_hsap_3774,
Macaca mulatta	ENSMMUG00000017596	1 retrocopy	retro_mmul_1640,
Pongo abelii	ENSPPYG00000002610	1 retrocopy	retro_pabe_3084 ,
Tupaia belangeri	ENSTBEG00000005555	1 retrocopy	retro_tbel_3660,
Tursiops truncatus	ENSTTRG00000012618	2 retrocopies	retro_ttru_138, retro_ttru_437,