RetrogeneDB ID: retro_nleu_2221

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397335.1:1557731..1558534(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAP1
• Ensembl ID: ENSNLEG00000012077
• Aliases: None
• Description: Adenylyl cyclase-associated protein [Source:UniProtKB/TrEMBL;Acc:G1RN97]

Sequence

>retro_nleu_2221
ATGACTGACATGCAAAATCTGGTAGAAAAATTGGACAGGGCAGTGGGCCGCCTGGAGGCAGTATCCCATACCTCTGACAT
GCACCGTGGATATGGAGATAGTCCTTCAAAAGCAGGAGCAGCTCCATATGCACAGGCATTTGACTCGCTGCTTGCCTGCC
CTGTGGCGGAGCACTTGAAGATCAGTAAAGAGATTGGGGGAGACATGCAGAAAGATGTGGAGATGGTCCACACAGGTTCG
AAGTTGGAGTGAGCTCTCTTGGTTACAGCTTCTCAGTGTCAACAGCCGGCAGGTAATAAGCTTTCCAATTTGTTGGCACC
TATCTCAGAGCAGATCAAAGAAGTGATAACCTTTTGGGAGAAGAACCGAGGCAGCAAGTTGATTAATCAGCTGTCAGCTG
TCAGCGAAAGTATCCAGGCCCTAGGCTGGGTGGCTATGGCTCCCAATCCTGGCCCTTATGTGAAAGAAATGAATCATGCT
GCCGTGTTTTATACAAACTGAGTCCTTAAAGAGTACAAAGATGTGGATAAGAAGCATGTAGACTGAGTCAAAGCTTATTT
AAGTATATGCACAGAGCTGCAGGCTTACATTAATGAGTTCCATACCACCAGACTGCCTGGAGCAAAACGGGGCCTGTGAC
AAAAGAACTGAGTGGACTGCCATCTGGACCCTCTGCTGCATCAGCTACTCCTCCCCCACCATCAAGCCTCCCTCCTCCAC
TAGTCTCTGTCAGTTCAGGCTCAGATGAGTCCGCTTCCCTCTCAGCACTGTTTGCGCAGGTTAATCAGCGGGAGAGCATC
ACA

Alignment

ORF - retro_nleu_2221 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.25 %
• Parental protein coverage: 56.42 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MADMQNLVERLERAVGRLEAVSHTSDMHRGYGDSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQ
          M.DMQNLVE.L.RAVGRLEAVSHTSDMHRGYGDSPSKAGAAPY.QAFDSLLA.PVAE.LKISKEIGGD.Q
Retrocopy MTDMQNLVEKLDRAVGRLEAVSHTSDMHRGYGDSPSKAGAAPYAQAFDSLLACPVAEHLKISKEIGGDMQ

Parental  KHAEMVHTGLKLERALLVTASQCQQPADNKLSDLLAPISEQIKEVITFREKNRGSKLFNHLSAVSESIQA
          K..EMVHTG.KLE.ALLVTASQCQQPA.NKLS.LLAPISEQIKEVITF.EKNRGSKL.N.LSAVSESIQA
Retrocopy KDVEMVHTGSKLE*ALLVTASQCQQPAGNKLSNLLAPISEQIKEVITFWEKNRGSKLINQLSAVSESIQA

Parental  LGWVAMAPKPGPYVKEMNDAAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGL-AWSK
          LGWVAMAP.PGPYVKEMN.AA.FYTN.VLKEYKDVDKKHVD.VKAYLSI.TELQAYI.EFHTT.L.AWSK
Retrocopy LGWVAMAPNPGPYVKEMNHAAVFYTN*VLKEYKDVDKKHVD*VKAYLSICTELQAYINEFHTTRL<AWSK

Parental  TGPVAKELSGLPSGPSAGSGPPPPPPGPPPPPVSTSSGSDESASRSALFAQINQGESIT
          TGPV.KELSGLPSGPSA.S..PPPP...PPP.VS.SSGSDESAS.SALFAQ.NQ.ESIT
Retrocopy TGPVTKELSGLPSGPSAASATPPPPSSLPPPLVSVSSGSDESASLSALFAQVNQRESIT

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_2221 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 10 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000003012	2 retrocopies	retro_cfam_1316, retro_cfam_645,
Homo sapiens	ENSG00000131236	2 retrocopies	retro_hsap_2666, retro_hsap_664,
Gorilla gorilla	ENSGGOG00000027527	2 retrocopies	retro_ggor_1860, retro_ggor_575,
Macropus eugenii	ENSMEUG00000004960	1 retrocopy	retro_meug_544,
Mus musculus	ENSMUSG00000028656	1 retrocopy	retro_mmus_1265,
Nomascus leucogenys	ENSNLEG00000012077	2 retrocopies	retro_nleu_1600, retro_nleu_2221 ,
Otolemur garnettii	ENSOGAG00000005492	1 retrocopy	retro_ogar_299,
Pongo abelii	ENSPPYG00000001496	4 retrocopies	retro_pabe_2212, retro_pabe_2358, retro_pabe_2415, retro_pabe_584,
Pan troglodytes	ENSPTRG00000000583	2 retrocopies	retro_ptro_1796, retro_ptro_484,
Rattus norvegicus	ENSRNOG00000013492	1 retrocopy	retro_rnor_1180,