RetrogeneDB ID: retro_pabe_2742

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:62307815..62308895(-)
• Located in intron of: ENSPPYG00000015490

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3L
• Ensembl ID: ENSPPYG00000020383
• Aliases: None
• Description: guanine nucleotide binding protein-like 3 (nucleolar)-like [Source:HGNC Symbol;Acc:25553]

Sequence

>retro_pabe_2742
GCTTTCAAGGCCAGGACCCAGCATCAGGTCAGCTTTGGAGCTGAAAACCTCACAAAGGTTCGGGAGAACTATTGCTGCCT
TGGTGAAGTGTGCACCCACATCCATATGGGCGTTGTGGGCCTTCCCAATATTGGGAAGAGCAGCCTGATTAAAAGCCTGA
AGTGCAGCCATGCATGCAGTGTGGGAGCCATTCCTGGGGTCACAAAATTCATGCAGGAGGTCCACCTGGACAAGTTCATC
TGGCTGCTGGATGCTCCAGCCATTGTTCCAGGGCCCAGCTCAGAGATGGGCACCATCCTGCATAACTGCATCCACATCTA
GAGGCTGGCAGACCCCATGACCCCAGTGGAGACCATCTTGCAGTGCTGCAACCTGGAGGAGATTTCCAACTATTACCTTC
TCTCTGGGTACCAGACTACTGAGCACTTTCTGATGGCAGTGGCCCACCATTTGGGGAAGAAGAGAGACTTACACAGTCAG
GCGCAGGCAGCCAAAGCTGTCCTAGATGACTGGGTGAGCGGGAAGATCAGCTTCTATAGACCACCACCACCCACTCACAC
TCTGCCCGCCCATCTCAGTGCTGAGATAATTAAGGAAATGACCAAGGTCTTTGACATCGAGGATACCGAGCAGGTCAATG
AAGACACCATGGAATGCTTGGCCACTGGAGAATCTGATGAGCTGTTGGGTGACACAGACCCACTCAAAATGGAGATCAAG
TTGCTCCATTCTCCGATGATGAAAATAGCAGATGCCATTGAAGATAAAGCTACTGTGTATAAGATTGGAGATCTCACTGG
TTATTGCACCAATCCGAATCATCATCAGATGGGGTGGGCTAAACTCAATGTAGACCACCACCCTAAAAAAAACAGTAAGG
TGGATGTGTGCCCAGTGGACTGCTGCCCAGTACTGCAGAGGATGATGGAAATGGACCCCCTACAACAGGGCCAGGCTCTG
GCATCCTCCCTGAAGAATAAGAATTTGCAGAAATGTGCAGATAAAATCCCCAGGGAGCTGTCTGATTCCATGATGTCTGC
TCTCCACCTCTCTGGCAATGCTGATGGCAGTGTTGGTGAC

Alignment

ORF - retro_pabe_2742 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.86 %
• Parental protein coverage: 70.35 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASESLLKSKACFGAENLMRVLGNYCRLGEVRTHIRVGVVGLPNVGKSSLINSLKRSRACGVGAVPGITKF
          A..........FGAENL..V..NYC.LGEV.THI..GVVGLPN.GKSSLI.SLK.S.AC.VGA.PG.TKF
Retrocopy AFKARTQHQVSFGAENLTKVRENYCCLGEVCTHIHMGVVGLPNIGKSSLIKSLKCSHACSVGAIPGVTKF

Parental  MQEVYLDKFIRLLDAPGIVPGPNSEVGTILRNCVHVQKLADPVTPVETILQRCNLEEISNYYGVSGFQTT
          MQEV.LDKFI.LLDAP.IVPGP.SE.GTIL.NC.H...LADP.TPVETILQ.CNLEEISNYY..SG.QTT
Retrocopy MQEVHLDKFIWLLDAPAIVPGPSSEMGTILHNCIHI*RLADPMTPVETILQCCNLEEISNYYLLSGYQTT

Parental  EHFLTAVAHRLGKKKKGGLYSQEQAAKAVLADWVSGKISFYIPPPATHTLPTHLSAEIVKEMTEVFDIED
          EHFL.AVAH.LGKK....L.SQ.QAAKAVL.DWVSGKISFY.PPP.THTLP.HLSAEI.KEMT.VFDIED
Retrocopy EHFLMAVAHHLGKKRD--LHSQAQAAKAVLDDWVSGKISFYRPPPPTHTLPAHLSAEIIKEMTKVFDIED

Parental  IEQANEDTMECLATGESDELLGDTDRLEMEIKLLHSPMTKIADAIENKTTVYKIGDLTGYCTNPNHHQMG
          .EQ.NEDTMECLATGESDELLGDTD.L.MEIKLLHSPM.KIADAIE.K.TVYKIGDLTGYCTNPNHHQMG
Retrocopy TEQVNEDTMECLATGESDELLGDTDPLKMEIKLLHSPMMKIADAIEDKATVYKIGDLTGYCTNPNHHQMG

Parental  WAKRNVDHRPKSNNMVDVCSVDRRPVLQRIMETDPLQQGQALASALKNKKKMQKRADKIASKLSDSMMSA
          WAK.NVDH.P.....VDVC.VD..PVLQR.ME.DPLQQGQALAS.LKN.K..QK.ADKI...LSDSMMSA
Retrocopy WAKLNVDHHPXXXSKVDVCPVDCCPVLQRMMEMDPLQQGQALASSLKN-KNLQKCADKIPRELSDSMMSA

Parental  LDLSGNADDGVGD
          L.LSGNAD..VGD
Retrocopy LHLSGNADGSVGD

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	0.28 RPM	4.20 RPM
SRP007412_cerebellum	0.49 RPM	7.78 RPM
SRP007412_heart	0.18 RPM	7.19 RPM
SRP007412_kidney	0.07 RPM	9.18 RPM
SRP007412_liver	0.06 RPM	5.36 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2742 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2742 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2742 has 4 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3327
Gorilla gorilla	retro_ggor_1296
Macaca mulatta	retro_mmul_2084
Callithrix jacchus	retro_cjac_1853

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Parental genes homology:

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

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000252	2 retrocopies	retro_cjac_1591, retro_cjac_1853,
Homo sapiens	ENSG00000130119	1 retrocopy	retro_hsap_3327,
Gorilla gorilla	ENSGGOG00000007550	1 retrocopy	retro_ggor_1296,
Microcebus murinus	ENSMICG00000010144	1 retrocopy	retro_mmur_662,
Macaca mulatta	ENSMMUG00000008231	1 retrocopy	retro_mmul_2084,
Nomascus leucogenys	ENSNLEG00000016233	1 retrocopy	retro_nleu_1672,
Oryzias latipes	ENSORLG00000014117	1 retrocopy	retro_olat_29,
Pongo abelii	ENSPPYG00000020383	1 retrocopy	retro_pabe_2742 ,