RetrogeneDB ID: retro_ptro_1404

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 20:46876158..46877345(+)
• Located in intron of: ENSPTRG00000023101

Retrocopy information

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

Parental gene information

• Parental gene symbol: GLYR1
• Ensembl ID: ENSPTRG00000007730
• Aliases: None
• Description: glyoxylate reductase 1 homolog (Arabidopsis) [Source:HGNC Symbol;Acc:24434]

Sequence

>retro_ptro_1404
TCCAAATCCCCTCTGAAAAGAATCCAAGAGCAAAGTCCCCAGAAGCGGGGTCAGCCCCCAAAGAATGAGAAGAATGTCAC
CATCCTGGAGTCCGGTACCTTGAAGTGGATGATGGCCGGACCAGTGGCTGCATTTAAATGGCAGCCGACCAGAAGCGAGC
CTGTTAAAGATGCAGATCCTCATTTCCATCATTTCCTGCTAAGCCAAACAGAAGCCATCTCTGTCTGTTACCAGGCAATC
ACAAAGAAGTTGAAAATATGTGAAGAGGAAACTGGTTCCACCTCCATCCGGGCAGCTGACAGCACGGCCGTGAATGGCAG
CATCACAGACAAAAAGATGGGATTTGGGGGCCTTGGTCGCATGAGAAGTGGAATCGTCTCTAACTTGCTAAAAATGGGTC
ACACAGTGACTGTCTGGAACCGCACTGCCAAGAAACGTGATTTGTTCATCTAGGAGGGGGCCTGCCTGGGAAGAACCCCT
GCTGAAGTCCTCTCAACCTGTGACATCACTTTCGCCCGTGTGTTGGATTCCAAGGCGGCCAGGGACCTGGTGCTGGGCCC
CAGTGGTATGCTGCAAGGGATCTGCCCTGGAAAGTGCTACGTGGACATGTCAACGGTGGACGCTGACATAGTCACTTAGC
TGGCCCGGGTGATTGCGTCCAGGTTGGGGGGTTGCTTTCCAGAAGCTCCCATCTCAGGGAATCAGCAGCTTTCTAATCAC
GGAATGTTGGTGATCTTAGCAGCTGGAGACAGGGGCCTATAGGAGGACTGCAGCAGCTGCTTCCAGGCAATAGGGAAGAC
CTCCTCCTTCCTAGGTGAAGTTGGCAACGCAGCCAAGATGATGCTGATCGTGAACATAGTCTAAGGGAGCTTCATAGCCA
TGATCACTGAGGTGCTGACCCTGGCCTAGGTGACAGATCAGGCCCAGCAGACACTCTTGGACATTCTCAATCAGGGACAG
TTGGCCAGCATCTTCCTAGTCCAGAAGTGCCAAAATACCCTGCAAGGAAACTTTAAGCCTGATTTCTACCAAAATACATG
CAGAAGGATCTCTGCTTAGCCATTGCGCTAGGCAATGTGGTCAACTGTCCGACTCCCATGGCAGCTGCAGCCAACCAGGT
GTACAAAAGAGCCAAGGCACTGGACCAGTCCAACAATATGTCCGCTGTGTCCTGAGCCTACATACAC

Alignment

ORF - retro_ptro_1404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.0 %
• Parental protein coverage: 80.24 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SKSPLKRAQEQSPRKRGRPPKDEKDLTIPESSTVKGMMAGPMAAFKWQPTASEPVKDADPHFHHFLLSQT
          SKSPLKR.QEQSP.KRG.PPK.EK..TI.ES.T.K.MMAGP.AAFKWQPT.SEPVKDADPHFHHFLLSQT
Retrocopy SKSPLKRIQEQSPQKRGQPPKNEKNVTILESGTLKWMMAGPVAAFKWQPTRSEPVKDADPHFHHFLLSQT

Parental  EKPAVCYQAITKKLKICEEETGSTSIQAADSTAVNGSITPTDKKIGFLGLGLMGSGIVSNLLKMGHTVTV
          E...VCYQAITKKLKICEEETGSTSI.AADSTAVNGSIT..DKK.GF.GLG.M.SGIVSNLLKMGHTVTV
Retrocopy EAISVCYQAITKKLKICEEETGSTSIRAADSTAVNGSIT--DKKMGFGGLGRMRSGIVSNLLKMGHTVTV

Parental  WNRTAEKCDLFIQEGARLGRTPAEVVSTCDITFACVSDPKAAKDLVLGPSGVLQGIRPGKCYVDMSTVDA
          WNRTA.K.DLFI.EGA.LGRTPAEV.STCDITFA.V.D.KAA.DLVLGPSG.LQGI.PGKCYVDMSTVDA
Retrocopy WNRTAKKRDLFI*EGACLGRTPAEVLSTCDITFARVLDSKAARDLVLGPSGMLQGICPGKCYVDMSTVDA

Parental  DTVTELAQVIVSR-GGRFLEAPVSGNQQLSNDGMLVILAAGDRGLYEDCSSCFQAMGKTSFFLGEVGNAA
          D.VT.LA.VI.SR.GG.F.EAP.SGNQQLSN.GMLVILAAGDRGL.EDCSSCFQA.GKTS.FLGEVGNAA
Retrocopy DIVT*LARVIASRLGGCFPEAPISGNQQLSNHGMLVILAAGDRGL*EDCSSCFQAIGKTSSFLGEVGNAA

Parental  KMMLIVNMVQGSFMATIAEGLTLAQVTGQSQQTLLDILNQGQLASIFLDQKCQNILQGNFKPDFYL-KYI
          KMMLIVN.V.GSF.A.I.E.LTLA.VT.Q.QQTLLDILNQGQLASIFL.QKCQN.LQGNFKPDFY..KY.
Retrocopy KMMLIVNIV*GSFIAMITEVLTLA*VTDQAQQTLLDILNQGQLASIFLVQKCQNTLQGNFKPDFYQ<KYM

Parental  QKDLRLAIALGDAVNHPTPMAAAANEVYKRAKALDQSDNDMSAVYRAYIH
          QKDL.LAIALG..VN.PTPMAAAAN.VYKRAKALDQS.N.MSAV..AYIH
Retrocopy QKDLCLAIALGNVVNCPTPMAAAANQVYKRAKALDQS-NNMSAVS*AYIH

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	0.04 RPM	44.36 RPM
SRP007412_cerebellum	0.11 RPM	63.67 RPM
SRP007412_heart	0.17 RPM	25.85 RPM
SRP007412_kidney	0.16 RPM	44.69 RPM
SRP007412_liver	0.03 RPM	28.41 RPM
SRP007412_testis	0.11 RPM	18.76 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_1404 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_1404 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_1404 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2432
Pongo abelii	retro_pabe_1791

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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 ,