RetrogeneDB ID: retro_pabe_1791

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 20:47554986..47556535(+)
• Located in intron of: ENSPPYG00000011119

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLYR1
• Ensembl ID: ENSPPYG00000007072
• Aliases: GLYR1, N-PAC, NP60
• Description: putative oxidoreductase GLYR1 [Source:RefSeq peptide;Acc:NP_001127519]

Sequence

>retro_pabe_1791
CCTCATGGAAAGAAATGCTTCTTTGTGAAATTTTTTTGGAACATAAGATCATGCCTGGATTAAAGTGAAACAGCTGAAGC
CATATCATGCTCATAAAGAGGAAATGATAAAGATTAACAAGGGTAAACTATTCCAGCAAGTGGTGGATGCCGCCAAAGAG
TTTCTCAGGAGAGCCCACAGGGAAAGATCAGACGTCATCCCACAATTCTGCTGATGACAAGCATCAGCTTAATTCCAGTG
AGGAGAGACGTGGGCCAAACTCAGGTGATGGGAAGTGCAAACAGCCTGTCTGAAGGGAAGGTGAAGAAGATCATGGGAGA
AGGAAAGAAGCGGGTGTCTTCGGGCTCTTCAGAGAGAGGCTCCAAATCCCCTCTGAAAAGAATCCAAGAGCAAAGTCCCC
AGAAGCGGGGTCAGCCCCCAAAGGATGAGAAGAATGTCACCATCCCGGAGTCCAGTACCTTGAAGTGGATGATGGCCAGA
CCAGTGGCCGCATTTAAATGGCAGCCGACCAGAAGCGAGCCTGTTAAAGATGCAGATCCTCATTTCCATCATTTCCTGCT
AAGCCAAACAGAAGCCATCTCTGTCTGTTACCAGGCAATCACAGAGAAGTTGAAAATATGTGAAGAGGAAATTGGTTCCA
CCTCCATCCGGGCAGCTGACAGCATGGCCATGAATGGCAGCATCACAGACAAAAAGGTAGGATTTGGGGGCCTTGGTCTT
AGGAGAAATGGAATCGTCTCTTAACTTGCTAAAAATGGGTCACACGGTGACTGTCGGGAACCGCACTGCCAAGAAACGTG
ATTTGTTCATTTAGGAGGGGGCCCGCCTGGGAAGAACCCCTGCTGAAGTCCTCTCAACCTGTGACATCACTTTCGCCCGT
GTGTTGGATCCCAAGGCAGCCAAGGACCTGGTGCTGGGCCCCAGTGGTATGCTGCAAGGGATCCGCCCTGGGAAGTGCTA
CGTGGACATGTCAACAGTGGACGCTGACATAGTCACTGAGCTGGCCCAGGTGATTGCGTCCAGGTCGGGGGGTCGCTTTC
CAGAAGCCCCCATCTCAGGGAATCAGCAGCTTTCTAATCATGGGATGTTGGTGATCTTAGCAGCTGGAGACAGGGGCCTA
TATGAGGACTGCAGCAGCTGCTTCCAGGTGATGGGGAAGACCTCCTTCTTCCTAGGTGAAGTTGGCAACCAAGCCAAGAT
GATGCTGATCGTGAACATAGTCCAAGGAAGCTTCATGGCCACGATCACCAAGGTGCTGATCCTAGCCTAGGTGACAGATC
AGTCCCAGCAGACACTCTTGGACATCCTCAATCAGGGGCAGTTGGCCAGCATCTTCCTAGACCAGAAGTGCCAAAATACC
CTGCAAGGAAACTTTAAGCCTGATTTCTACCTGAAATACATGCAGAAGGATCTCTGCTTAGCCATTGCGCTGGGCAATGC
GGTCAACCATCCGACTCCCATGGCATCTGCAGCCAGCGAGGTGTACAAAAGAGCCAAGGCACTGGACCAGTCCGACAATA
TGTCTGCTGTGTCCCGAGCCTACATACAC

Alignment

ORF - retro_pabe_1791 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.05 %
• Parental protein coverage: 90.05 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PRGKKCFFVKFF-GTEDHAWIKVEQLKPYHAHKEEMIKINKGKRFQQAVDAVEEFLRRA-KGKDQTSSHN
          P.GKKCFFVKFF.GT.DHAWIKV.QLKPYHAHKEEMIKINKGK.FQQ.VDA..EFLRRA..GKDQTSSHN
Retrocopy PHGKKCFFVKFF>GT*DHAWIKVKQLKPYHAHKEEMIKINKGKLFQQVVDAAKEFLRRA>TGKDQTSSHN

Parental  SSDDKNRRNSSEERSRPNSGDEKRKLSL-SEGKVKKNMGEGKKRVSSGSSERGSKSPLKRAQEQSPRKRG
          S.DDK...NSSEER..PNSGD.K.K.....EG......G..K.....G........P............G
Retrocopy SADDKHQLNSSEERRGPNSGDGKCKQPV*REG--EEDHGRRKEAGVFGLFRERLQIPSEKNPRAKSPEAG

Parental  RPPK-DEKDLTIPESSTVKGMMAGPMAAFKWQPTATEPVKDADPHFHHFLLSQTEKPAVCYQAITKKLKI
          ..PK.DEK..TIPESST.K.MMA.P.AAFKWQPT..EPVKDADPHFHHFLLSQTE...VCYQAIT.KLKI
Retrocopy SAPK>DEKNVTIPESSTLKWMMARPVAAFKWQPTRSEPVKDADPHFHHFLLSQTEAISVCYQAITEKLKI

Parental  CEEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGLMGSGIVS-NLLKMGHTVTVWNRTAEKCDLFIQEG
          CEEE.GSTSI.AADS.A.NGSI..TDKK.GF.GLGL...GIVS.NLLKMGHTVTV.NRTA.K.DLFI.EG
Retrocopy CEEEIGSTSIRAADSMAMNGSI--TDKKVGFGGLGLRRNGIVS>NLLKMGHTVTVGNRTAKKRDLFI*EG

Parental  ARLGR-PAEV-STCDITFACVSDPKAAKDLVLGPSGVLQGIRPGKCYVDMSTVDADTVTELAQVIVSR-G
          ARLGR.PAEV.STCDITFA.V.DPKAAKDLVLGPSG.LQGIRPGKCYVDMSTVDAD.VTELAQVI.SR.G
Retrocopy ARLGRTPAEVLSTCDITFARVLDPKAAKDLVLGPSGMLQGIRPGKCYVDMSTVDADIVTELAQVIASRSG

Parental  GRFLEAPVSGNQQLSNDGMLVILAAGDRGLYEDCSSCFQAMGKTSFFLGEVGNAAKMMLIVNMVQGSFMA
          GRF.EAP.SGNQQLSN.GMLVILAAGDRGLYEDCSSCFQ.MGKTSFFLGEVGN.AKMMLIVN.VQGSFMA
Retrocopy GRFPEAPISGNQQLSNHGMLVILAAGDRGLYEDCSSCFQVMGKTSFFLGEVGNQAKMMLIVNIVQGSFMA

Parental  TIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNILQGNFKPDFYLKYIQKDLRLAIALGDAVNH
          TI...L.LA.VT.QSQQTLLDILNQGQLASIFLDQKCQN.LQGNFKPDFYLKY.QKDL.LAIALG.AVNH
Retrocopy TITKVLILA*VTDQSQQTLLDILNQGQLASIFLDQKCQNTLQGNFKPDFYLKYMQKDLCLAIALGNAVNH

Parental  PTPMAAAANEVYKRAKALDQSDNDMSAVYRAYIH
          PTPMA.AA.EVYKRAKALDQSDN.MSAV.RAYIH
Retrocopy PTPMASAASEVYKRAKALDQSDN-MSAVSRAYIH

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	0.06 RPM	133.14 RPM
SRP007412_cerebellum	0.36 RPM	76.37 RPM
SRP007412_heart	0.18 RPM	36.88 RPM
SRP007412_kidney	0.10 RPM	89.63 RPM
SRP007412_liver	0.09 RPM	29.90 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1791 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1791 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1791 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2432
Pan troglodytes	retro_ptro_1404

---

Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019912	1 retrocopy	retro_cjac_2514,
Erinaceus europaeus	ENSEEUG00000011783	1 retrocopy	retro_eeur_477,
Homo sapiens	ENSG00000140632	1 retrocopy	retro_hsap_2432,
Gorilla gorilla	ENSGGOG00000016258	1 retrocopy	retro_ggor_1512,
Macaca mulatta	ENSMMUG00000009567	1 retrocopy	retro_mmul_621,
Nomascus leucogenys	ENSNLEG00000009950	1 retrocopy	retro_nleu_240,
Oryctolagus cuniculus	ENSOCUG00000010486	1 retrocopy	retro_ocun_680,
Pongo abelii	ENSPPYG00000007072	1 retrocopy	retro_pabe_1791 ,
Pan troglodytes	ENSPTRG00000007730	1 retrocopy	retro_ptro_1404,