RetrogeneDB ID: retro_nleu_1035

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397279.1:24442959..24444355(+)
• Located in intron of: ENSNLEG00000017575

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAMM50
• Ensembl ID: ENSNLEG00000015693
• Aliases: None
• Description: None

Sequence

>retro_nleu_1035
ATGAGGACATTGTACACCCCGAGTTTGGAGCCTCTTCCACCAAAAGGATCTGGCTTTGGAGCATCAGAAAATGAAACTGA
ATTTGCTGAAGGTGAAAATGAAGCTAAACAGTAAATTCTTAAAAACAAAGATTTGGCTGTTCAACATGCCCATTTCGATG
GGCTTGGGTGGACTAAATAAAGATAATATCACCATTTGTAAAACTGGAGATTTTTTTAAGGCTAAAAACCTCATTGAGGT
AATGTGGAACTCTCATGAAGCCTGTGGAAAATTTCTTCATCCAGGAATTTTTTAGACAAGTGGATTTTTTGAGTGATACA
TATCAAGGTGACAATGCATTTCCAAATGGGTTAGATGTTACCTTTGAAGTAACTGAATTAAGGAAATTAATGGGCAGTTA
AAACACCATGGTTGGAAACAATGAAGGGAGTCTGGTACTTGGCCTCAAACTCCCTAATCTTCTAGGTTATGCAGAAAAGG
TGACTTTTCATTTTTCCCATGGAACAAAAGAAACTTCCCATGGCCTTTCTTCAAACCATGGCCTAGAAACTTCAAAAGGA
ATTTACCCGTAAACTTACATAAAGTTACTGAACAGTTCCCTTGGAGTTCACTTCCGGAGATGAACAGAAGATGATCAGCC
AAGTACAGTCTTCCCATATGAAAGACCAGCCACACCATCAATTGGAAAGGCATGTGGCGAGACCTGGGCTGCCACTTAAG
GACAGCATCATTTGCTGTTTGAAAGTAAGGCAGACATTCACTTAAATCATATCTTTCACATGCCATGGTCATCGATTTTC
AGAATTCTTCCATCTTACCAAGAAAATGTGTTTTGCTGAAAGTTAACCAGGAACTGACAGGCTACACGACAAGGGATATA
AGCTTCATCAAAGATTTTGAACTTCAGTTGAATAAACCACTCATATTTGATTCAGTTTTTTCAGCATTTCTCTGAGGTGG
GATGTTGGCACCCATGGTGATAAACTGTGAGTCCTGCTGATAGTTTCACCTTGGGGGACCAACAAGTGTCCAAGGATTCA
GCATGCACAGCACCGGAGCAGAGTGCAGGCGACCACCTAGGTGCAGAAGCACGCTGGGCCAGCGGCCTGCATCTGTATAC
CCCAACACGTTTAAAGCCAAGCCAGGGCAGTTTGGGAGAACTTTTCCAAACACTTTTTTCTCAACACAGGAAACCTCTGC
AACCTCAACTATGGAGAGGGCCCCAAAGCGTATTCGTGAGCTGGCTGAATGCATCTGCCAGTTTTATGGCACCAGGATTG
TCTTTAGGCTTGGCAACATGGCTCTGTTGGAACTTAATTACTACTTTCCTATGGGAGTGCAGACAGGCAACAGCATATGT
GATAGCATTTAGTTTTGAGCTGGGATAAGGTTCCTG

Alignment

ORF - retro_nleu_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 9
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  MGTVHARSLEPLPSSGPDFGGLGEEAEFVEVEPEAKQEILENKDVVVQHVHFD-GLGR-TKDDIIICEIG
          M.T....SLEPLP..G..FG....E.EF.E.E.EAKQ.IL.NKD..VQH.HFD.GLG...KD.I.IC..G
Retrocopy MRTLYTPSLEPLPPKGSGFGASENETEFAEGENEAKQ*ILKNKDLAVQHAHFD>GLGGLNKDNITICKTG

Parental  DVFKAKNLIEVMRKSHEAREKLLRLGIF-RQVDVLIDTCQGDDALPNGLDVTFEVTELRRLTGSYNTMVG
          D.FKAKNLIEVM..SHEA..K.L..GIF.RQVD.L.DT.QGD.A.PNGLDVTFEVTELR.L.GS.NTMVG
Retrocopy DFFKAKNLIEVMWNSHEACGKFLHPGIF>RQVDFLSDTYQGDNAFPNGLDVTFEVTELRKLMGS*NTMVG

Parental  NNEGSMVLGLKLPNLLGRAEKVT-FQFSYGTKETSYGLSFFKPRPGNFERNFSVNLYKVTGQFPWSSLRE
          NNEGS.VLGLKLPNLLG.AEKVT.F.F............FFKP.P.NF.RN..VNL.KVT.QFPWSSL.E
Retrocopy NNEGSLVLGLKLPNLLGYAEKVT<FSF-FPWNKRNFPWPFFKPWPRNFKRNLPVNLHKVTEQFPWSSLPE

Parental  TDRGMSAEYSFPIWKTSHTVKWEGVWRELGCLSRTASFAVRKESGHSLKSSLSHAMVIDSRNSSILPRRG
          ..R..SA.YS.PI.KTSHT..W.G.WR.LGC..RTASFAV.K...HSLKS.LSHAMVID..NSSILPR..
Retrocopy MNRR*SAKYSLPI*KTSHTINWKGMWRDLGCHLRTASFAV*K*GRHSLKSYLSHAMVIDFQNSSILPRKC

Parental  ALLKVNQELAGYTGGDVSFIKEDFELQLNKQLIFDSVFSASLWGGMLVPI-GDK-PSSIADRFYLGGPTS
          .LLKVNQEL.GYT..D.SFIK.DFELQLNK.LIFDSVFSA.L.GGML.P..GDK...S.AD.F.LG....
Retrocopy VLLKVNQELTGYTTRDISFIK-DFELQLNKPLIFDSVFSAFL*GGMLAPM<GDK<TVSPADSFTLGDQ-Q

Parental  VRGFSMHSIGPQSEGDYLGGEAYWAGGLHLYTPLPFRPGQGG-FG-ELFRTHFFLNAGNLCNLNYGEG-P
          V...S......QS.GD.LG.EA.WA.GLHLYTP....P.QG..FG.E.F..HFFLN.GNLCNLNYGEG.P
Retrocopy VSKDSACTAPEQSAGDHLGAEARWASGLHLYTPTRLKPSQGS<FG<ENFSKHFFLNTGNLCNLNYGEG>P

Parental  KAHIRKLAECIRWSYGAGIVLRLGNIARLELNYCIPMGVQTGDRICDGVQFGAGIRFL
          K..IR.LAECI...YG..IV.RLGN.A.LELNY..PMGVQTG..ICD...F.AGIRFL
Retrocopy K-RIRELAECICQFYGTRIVFRLGNMALLELNYYFPMGVQTGNSICDSI*F*AGIRFL

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Nomascus leucogenys was not studied using RNA-Seq expression data.

ChIP-Seq

Nomascus leucogenys was not studied using ChIP-Seq data.

EST

Nomascus leucogenys was not studied using EST data.

TSS

Nomascus leucogenys was not studied using FANTOM5 data.

Lab

retro_nleu_1035 was not experimentally validated.

Homology

Retrocopy orthology:

Nomascus leucogenys does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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Parental genes homology:

Parental genes homology involve 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015070	2 retrocopies	retro_cjac_2277, retro_cjac_605,
Homo sapiens	ENSG00000100347	1 retrocopy	retro_hsap_4233,
Macaca mulatta	ENSMMUG00000015446	1 retrocopy	retro_mmul_1152,
Nomascus leucogenys	ENSNLEG00000015693	1 retrocopy	retro_nleu_1035 ,
Pongo abelii	ENSPPYG00000011918	1 retrocopy	retro_pabe_3404,
Pan troglodytes	ENSPTRG00000014483	1 retrocopy	retro_ptro_2876,