RetrogeneDB ID: retro_nleu_403

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397264.1:58349836..58350936(+)
• Located in intron of: ENSNLEG00000017962

Retrocopy information

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

Parental gene information

• Parental gene symbol: SEC14L1
• Ensembl ID: ENSNLEG00000007634
• Aliases: None
• Description: None

Sequence

>retro_nleu_403
TGCTATACCGTTCACCCTGAAAATGAAGATTGGACCTGTTTTGAACAGTCTGCAAGTTTAGATATTAAATCTTTCTTTGG
TTTTGAAAGTACCGTGGAAAAAATTGCAATGAAACAATATACCAGCAACATTAAAAAAAGGAAAGGAAATCATTGAATAC
TACCTTTGCCATTTAGAAGAAGGCATAACCTTTGTGCCCCGCTGGACTCCGCCTTCCATCACGCCCTCTTCAGAGACATC
TTCATCATCCTGCAAGAAACAAGCAGCGTCCATGGCCGTTGTCATCCCAGGTGCTGTCCTCAAGGAGGGGCTGAGTGGCG
ATGCCCTCAGCAGCCCCAGCGCACCTGAGCCCGTGGTGAGCACCCCTGATAACAAACTAGATGCTGACTACATCAAGAGA
TACCTGGGCGATTTGACTCCACTGCAGGAGAGCTGTCTCATTAGACTTCACCGGTGGCTCCAGAAGACCCACAAGGGCGA
AATTCCAAAAGATGAACATATTCTTCAGTTCCTACGTGCACAGGATTTTAAAATTGACAAAACCAGAGAGATCATTTGTC
AATCTTTGACGTGGAGGAAGCAGCACCAGGTAGACTACATTCTTGCTACCTGGACCGCTCCACAGGTCCTTCAGGATTAC
TACACGGGAGGCTGGCATCATCACGACAAAGATGGGCGGCCCTCTGTGTGCTCAGGCTGGGGCAGATGGACACCAACGGC
TTGGTGAGAGCTCTCGGGGAGGAAGCCCTGCCGAGATACGTTCTCTCCATAAATGAAGAAGAGCTAAGGCAATGTGAAGA
GAATACAAAAGTCTTTGTTCGGCCTATCAGCTCATGGACCTGCCTGGTGGACTTGGAAGGGGTGAACATGCGTCACTTGT
GGAGACTTGATGTCAAAGCTCTGCAGTGAATCATCGAGGTGGTGAAGGCCAATTACCCTAAGAGACTGAGCCGACTTCTC
ATCCTGCGGGCACCCAGGGTATTTCCGTGCTCTGGACGCTGGTTAGTCCATTTATTGATGACAACACCAGAAGGAAATTC
CTCATTTATGCAGGAAATGACTACCAGGGTCCTGGAGGCCTGATGGATTACATTGACAGA

Alignment

ORF - retro_nleu_403 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.95 %
• Parental protein coverage: 51.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  CYTVHPENEDWTCFEQSASLDIKSFFGFESTVEKIAMKQYTSNIKK-GKEIIEYYLRQLEEEGITFVPRW
          CYTVHPENEDWTCFEQSASLDIKSFFGFESTVEKIAMKQYTSNIKK.GKEIIEYYL..L.EEGITFVPRW
Retrocopy CYTVHPENEDWTCFEQSASLDIKSFFGFESTVEKIAMKQYTSNIKK>GKEIIEYYLCHL-EEGITFVPRW

Parental  TPPSITPSSETSSSSCKKQAVSMAVVIPDAALKEGLSGDALSSPSAPEPVVGTPDDKLDADYIKRYLGDL
          TPPSITPSSETSSSSCKKQA.SMAVVIP.A.LKEGLSGDALSSPSAPEPVV.TPD.KLDADYIKRYLGDL
Retrocopy TPPSITPSSETSSSSCKKQAASMAVVIPGAVLKEGLSGDALSSPSAPEPVVSTPDNKLDADYIKRYLGDL

Parental  TPLQESCLIRLRQWLQETHKGKIPKDEHILRFLRARDFNIDKAREIMCQSLTWRKQHQVDYILETWTPPQ
          TPLQESCLIRL..WLQ.THKG.IPKDEHIL.FLRA.DF.IDK.REI.CQSLTWRKQHQVDYIL.TWT.PQ
Retrocopy TPLQESCLIRLHRWLQKTHKGEIPKDEHILQFLRAQDFKIDKTREIICQSLTWRKQHQVDYILATWTAPQ

Parental  V-QDYYAGGWHHHDKDGRP-LYVLRLGQMDTKGLVRALGEEALLRYVLSINEEGLRRCEENTKVFGRPIS
          V.QDYY.GGWHHHDKDGRP.L.VLRLGQMDT.GLVRALGEEAL.RYVLSINEE.LR.CEENTKVF.RPIS
Retrocopy VLQDYYTGGWHHHDKDGRP<LCVLRLGQMDTNGLVRALGEEALPRYVLSINEEELRQCEENTKVFVRPIS

Parental  SWTCLVDLEGLNMRHLWRPGVKALLRIIEVVEANYPETLGRLLILRAPRVFP-VLWTLVSPFIDDNTRRK
          SWTCLVDLEG.NMRHLWR..VKAL..IIEVV.ANYP..L.RLLILRAPRVFP.VLWTLVSPFIDDNTRRK
Retrocopy SWTCLVDLEGVNMRHLWRLDVKALQ*IIEVVKANYPKRLSRLLILRAPRVFP<VLWTLVSPFIDDNTRRK

Parental  FLIYAGNDYQGPGGLLDYIDK
          FLIYAGNDYQGPGGL.DYID.
Retrocopy FLIYAGNDYQGPGGLMDYIDR

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_403 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000129657	1 retrocopy	retro_hsap_777,
Nomascus leucogenys	ENSNLEG00000007634	1 retrocopy	retro_nleu_403 ,
Pongo abelii	ENSPPYG00000008673	1 retrocopy	retro_pabe_752,