RetrogeneDB ID: retro_nleu_2687

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397398.1:2905870..2906869(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VPS37A
• Ensembl ID: ENSNLEG00000002558
• Aliases: None
• Description: None

Sequence

>retro_nleu_2687
AATTAACATATACTGCTTCCTCCACAATTTCCTCAGGAAAAACCAGTGATCAGTGTTTTTCCACCAATACGACATCACTT
AATGGATAAACAAGGAGTGTATGTTACTTCTCCATTAGCAAACAATTTTACAATGCGCTCAAATCTTGGAAAAATTATTC
AGAGTGTGTTGGATGAGTTTTGGAAGAATCCTCCAGTTTTAGCTCCTACTGCAACAGTATTTCCTTACCTATATAGTAAC
CCAAGTGGGATGCCTCCTTATGCTTCTCAAGCTTTTCCATTTCTTCCTCCATATCCCCCAGAAGAAGCAAAGAGGAGTAT
CACTTCTTTATCTGTTGCTAACACTGTTTCTTCTTCAACAAGTCATACCACAGCCAAGCCCGTCGCTCCCTCATTTGGCA
TCCTTTCAAATCTGCCATTACCCATTTCCACAACAGATGCTTCAATATTGACAAGCCAAAATGGTTTTGGTTACAAGATG
CCAGATGTCTCTGATGCATTTCCAGAACTCTCAGAACTAAGTGTGTCACGACTCACAGATATGAATGAACAAGAGGAGGT
ATTACTAGAACAGTTTCTGACTTTGTCTCGACTAAAACAAATTATTACTGACAAAGATGACTTAGTAAAAAGTATTGAGG
AACTAGCAAGAAAAAAATCTCCTTTTGGAGCCCAGCTTGGGAGCCAAAAGGCAAACTGTTTTAGATAAGTATGAATTACT
TAAACAAATGAAGTCTGCTTTCGAAAAGAAGATGCAAAGGCAGCGTGAACTTAGTGAGAGCTGTAGTGCAAGTGCCCTAC
AGGCAAGATTGAAAGTAGCTGCATATGAAGCTGGGGAAGAACCTGATAATATTGCGTAAGACTTCGTGGAGGGAAAAATG
GAAATAAGTGATTTTCTCAGTAGCTTCATGGAAAAGAGAACAATTTGCCACTGTAGAAGAGCCAGTAGCAATGCTATCAG
CAGGCAATAGCAATGCATAGCCAATTTCATGCTCCACTA

Alignment

ORF - retro_nleu_2687 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.1 %
• Parental protein coverage: 84.13 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NINILLPPQFPQEKPVISVYPPIRHHLMDKQGVYVTSPLVNNFTMHSDLGKIIQSLLDEFWKNPPVLAPT
          N..ILLPPQFPQEKPVISV.PPIRHHLMDKQGVYVTSPL.NNFTM.S.LGKIIQS.LDEFWKNPPVLAPT
Retrocopy N*HILLPPQFPQEKPVISVFPPIRHHLMDKQGVYVTSPLANNFTMRSNLGKIIQSVLDEFWKNPPVLAPT

Parental  STAFPYLYSNPSGMPPYASQGFPFLPPYPPQEANRSITSLSVADTVSSSTTSHTTAKPAAPSFGVLSNLP
          .T.FPYLYSNPSGMPPYASQ.FPFLPPYPP.EA.RSITSLSVA.TVSSS.TSHTTAKP.APSFG.LSNLP
Retrocopy ATVFPYLYSNPSGMPPYASQAFPFLPPYPPEEAKRSITSLSVANTVSSS-TSHTTAKPVAPSFGILSNLP

Parental  LPIPTMDASISTSQNGFGYKMPDVPDAFPELSELSVSQLTDMNEQEEVLLEQFLTLPQLKQIITDKDDLV
          LPI.T.DASI.TSQNGFGYKMPDV.DAFPELSELSVS.LTDMNEQEEVLLEQFLTL..LKQIITDKDDLV
Retrocopy LPISTTDASILTSQNGFGYKMPDVSDAFPELSELSVSRLTDMNEQEEVLLEQFLTLSRLKQIITDKDDLV

Parental  KSIEELAR-KNLLLEPSLEAKRQTVLDKYELLTQMKSTFEKKMQRQHELSESCSASALQARLKVAAHEAE
          KSIEELAR.KNLLLEPSL.AKRQTVLDKYELL.QMKS.FEKKMQRQ.ELSESCSASALQARLKVAA.EA.
Retrocopy KSIEELAR>KNLLLEPSLGAKRQTVLDKYELLKQMKSAFEKKMQRQRELSESCSASALQARLKVAAYEAG

Parental  EESDNIAEDFLEGKMEIDDFLSSFMEKRTICHCRRAKEEKL-QQAIAMHSQFHAPL
          EE.DNIA.DF.EGKMEI.DFLSSFMEKRTICHCRRA......QQAIAMHSQFHAPL
Retrocopy EEPDNIA*DFVEGKMEISDFLSSFMEKRTICHCRRASSNAI<QQAIAMHSQFHAPL

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_2687 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.

---

Parental genes homology:

Parental genes homology involve 8 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000682	2 retrocopies	retro_chof_1257, retro_chof_2124,
Callithrix jacchus	ENSCJAG00000011769	1 retrocopy	retro_cjac_1790,
Dipodomys ordii	ENSDORG00000014879	9 retrocopies	retro_dord_257, retro_dord_294, retro_dord_542, retro_dord_544, retro_dord_580, retro_dord_598, retro_dord_631, retro_dord_668, retro_dord_751,
Homo sapiens	ENSG00000155975	1 retrocopy	retro_hsap_3256,
Gorilla gorilla	ENSGGOG00000011650	1 retrocopy	retro_ggor_2217,
Nomascus leucogenys	ENSNLEG00000002558	1 retrocopy	retro_nleu_2687 ,
Pongo abelii	ENSPPYG00000018386	2 retrocopies	retro_pabe_2699, retro_pabe_2821,
Pan troglodytes	ENSPTRG00000020019	1 retrocopy	retro_ptro_2202,