RetrogeneDB ID: retro_nleu_3075

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397813.1:59210..60175(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SH3GL1
• Ensembl ID: ENSNLEG00000003122
• Aliases: None
• Description: None

Sequence

>retro_nleu_3075
AAGGCATTGACAGAAATGCTGGCAAGGACCATCAAGTACCTGCAGCCCAACCCAGCCTCGCAGGCTAAGCTGACCATGCT
CAACACGGTGTGCAAGATCCGGGGCCAGGTGAAGAACCCCGGCTACCCGCAGTCGGAGGGGCTCCTGAGCCAGTGCCTGA
TCTGCCACCAGAAGGAGCTGGGCAACGAGTCCAACTTCAGTGACGCACTGCTGGATGCCGGCGAGTCCATGAAGCACCCG
GCAGAGGTGAAGAACTCCCTGGACATAGAGGTCAAGCAGAACTTCATTGACTTCCTCCAGAACCTGTGTGAGAAAGACCT
GAAGGGGATCCAGCACCACGTGCAGAAGCTGGAGGGCCGCCGCCTGGACTTTGACTAAAAGAAGCAGCAGGGCGAGATCC
CCGATGAGGAGCTGCGCCAGGCACTGGAGAAGCTTGAGGACTCCAAGGAGGTAGCAGAAACCAGCATGCACAACCTCCTG
GAGACCGACACTGAGCAGGTGAGTCAACTCCCGGCCCTGGTGGAGGCGCAGCCGGACTACCACTGGCAGGCCATGCAGAT
CCTGGACGAGCTGGCAGAGAAGCTCCAGCACAGATGCGGGAAGCTTCCTCACACCTCAAGCGGGAGTATAAGCCCAAGTC
CTGGGAGCCCTTTGACCTCGGAGAGCCTGAGGAGTCCAACAGGGGCTTCCCCTGCACCACACTCCCCAAGATCGCAGCTT
CATCCTCTTTCCGATCTTCTGACAAGCCCATTTGGACTCCTAGCAGGAGCGTGCCGCCCCGAGAACAGCCAAGCTGCAAG
GTGCTGTACGACTTCCAGCCTGAGAACGATGGGGAGCTGGGCTTCCATGAGGGCGATGTCTTCATGCTGATCAACCAGAT
CAACGAGAACTGGTACCAGGGCCTGCTGGACGTCCAGTCGGGCTTCTCCCTGCTCAGCTACGTGGATGTGCTCGTGCCTC
TGCCC

Alignment

ORF - retro_nleu_3075 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.79 %
• Parental protein coverage: 97. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAVTEVLARTIEYLQPNPASRAKLTMLNTVSKIRGQVKNPGYPQSEGLLGECMIRHGKELGCESNFGDAL
          KA.TE.LARTI.YLQPNPAS.AKLTMLNTV.KIRGQVKNPGYPQSEGLL..C.I.H.KELG.ESNF.DAL
Retrocopy KALTEMLARTIKYLQPNPASQAKLTMLNTVCKIRGQVKNPGYPQSEGLLSQCLICHQKELGNESNFSDAL

Parental  LDAGESMKRLAEVKDSLDIEVKQNFIDPLQNLCEKDLKEIQHHLKKLEGRRLDFDYKKKRQGKIPDEELR
          LDAGESMK..AEVK.SLDIEVKQNFID.LQNLCEKDLK.IQHH..KLEGRRLDFD..KK.QG.IPDEELR
Retrocopy LDAGESMKHPAEVKNSLDIEVKQNFIDFLQNLCEKDLKGIQHHVQKLEGRRLDFD-*KKQQGEIPDEELR

Parental  QALEKFEESKEVAETSMHNLLETDIEQVSQLSALVDAQLDYHRQAVQILDELAEKLKRR-MREASSRPKR
          QALEK.E.SKEVAETSMHNLLETD.EQVSQL.ALV.AQ.DYH.QA.QILDELAEKL..R.MREASS..KR
Retrocopy QALEKLEDSKEVAETSMHNLLETDTEQVSQLPALVEAQPDYHWQAMQILDELAEKLQHR<MREASSHLKR

Parental  EYKPKPREPFDLGEPEQSNGGFPCTTAPKIAASSSFRSSDKPIRTPSRSMPPLDQPSCKALYDFEPENDG
          EYKPK..EPFDLGEPE.SN.GFPCTT.PKIAASSSFRSSDKPI.TPSRS.PP..QPSCK.LYDF.PENDG
Retrocopy EYKPKSWEPFDLGEPEESNRGFPCTTLPKIAASSSFRSSDKPIWTPSRSVPPREQPSCKVLYDFQPENDG

Parental  ELGFREGDVITLTNQIDENWYEGMLDGQSGFFPLSYVEVLVLLP
          ELGF.EGDV..L.NQI.ENWY.G.LD.QSGF..LSYV.VLV.LP
Retrocopy ELGFHEGDVFMLINQINENWYQGLLDVQSGFSLLSYVDVLVPLP

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_3075 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000141985	3 retrocopies	retro_hsap_1742, retro_hsap_1745, retro_hsap_1859,
Gorilla gorilla	ENSGGOG00000008198	3 retrocopies	retro_ggor_2151, retro_ggor_2258, retro_ggor_675,
Macaca mulatta	ENSMMUG00000000273	1 retrocopy	retro_mmul_1264,
Monodelphis domestica	ENSMODG00000000931	1 retrocopy	retro_mdom_1530,
Nomascus leucogenys	ENSNLEG00000003122	2 retrocopies	retro_nleu_2914, retro_nleu_3075 ,
Pongo abelii	ENSPPYG00000009405	6 retrocopies	retro_pabe_1488, retro_pabe_1516, retro_pabe_1530, retro_pabe_1542, retro_pabe_1700, retro_pabe_3542,