RetrogeneDB ID: retro_nleu_1600

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397300.1:17452104..17453260(-)
• 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_1600
ATGGCTGACATGCAAAATCTGGTAGAAAGATTGGAGGGGGCAGTGGGCCGCCTGGAGGCAGTATCTCATACCTCTGACAT
GCACCGTGGGTATGCAGACAGTTCTTCAAAAGTAGGAGCAGCTCCATATGTGCAGGCATTTGACTCGCTGCTTGCTGGTC
CTGTGGCAGAGTACTTGAAGATCAGTAAAGAGATTGGGGGAGACATGCAGAAACATGCGGAGATGGTCCACACAGGTTTG
AAGTTGGAGCGAGCTCTGTTGGTTACAGCTTCTCAGTGTCAACAACCAGCAGATAATAAGCTTTCTGACCTGTTGGCACC
CATCTCAGAGCAGATCAAAGAAGTGATAACCTTTCGGGAGAAGAACTGAGGCAGCAAGTTGTTTAATCACCTGTCAGCTG
TCAGCGAAAGTATCCAGGCCCTGGGCTGGGTGGCTATGGCTCCCAAGCCTGGCCCTTATGTGAAATAAATGAATGATCTG
CCATGTTTTATACAAACCGAGTCCTCAAAGAGTACAAAGATGTGGATAAGAAGCATGTAGACTGGGTCAAAGCTTATTTA
AGTATATGGACAGAGCTGCAGGCTTGCATTAAGGAGTTCCATACCACCAGACTGGCCTGGGGCAAAACGGGGCCTGTGGG
AAAAGAACTGAGTGGACTGCCATCTGGACCCTCTGCCGGATCAGGTCCTCCTCCCCCTCCACCAGGATCCCCTCCTCCCC
CAGTCTCTACCAGTTCAGGCTCAGATGAGTCCGCTTCCCACTCAGCACTGTTTGTGCAGATTAACCAGGGGGAGAGCATC
ACACATGCCCTGAAACATTATCTGATGACATGAAGACTCACAAGAACCCTGCCCTGAAGGCTCAGAGTGGTCCACTACGC
AGTGGCCCCAAGCCATTCTCTGCACCTAAACCCCAAACCAGCCCATCCCCCAAACCAGCCACAAAGAAGGAGCCAGCTAT
ACTTGAACTGGAGGGCAAGAAGTGGAGAGTGGAAAATCAGGAAAATGTTTCCAACCTGGTGATTGAGGACACAGAGCTGA
AACAGGTGGCTTACATATACAAGTGTGTCAACACGACATTGCAAATCAAGGGCAAAATTAGCTCCATTACAGTAGACAAC
CGTAAGAAACTTGGTCTGGTATTCAATGATGTGGTA

Alignment

ORF - retro_nleu_1600 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.3 %
• Parental protein coverage: 81.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MADMQNLVERLERAVGRLEAVSHTSDMHRGYGDSPSKAGAAPYVQAFDSLLAGPVAEYLKISKEIGGDVQ
          MADMQNLVERLE.AVGRLEAVSHTSDMHRGY.DS.SK.GAAPYVQAFDSLLAGPVAEYLKISKEIGGD.Q
Retrocopy MADMQNLVERLEGAVGRLEAVSHTSDMHRGYADSSSKVGAAPYVQAFDSLLAGPVAEYLKISKEIGGDMQ

Parental  KHAEMVHTGLKLERALLVTASQCQQPADNKLSDLLAPISEQIKEVITFREKNRGSKLFNHLSAVSESIQA
          KHAEMVHTGLKLERALLVTASQCQQPADNKLSDLLAPISEQIKEVITFREKN.GSKLFNHLSAVSESIQA
Retrocopy KHAEMVHTGLKLERALLVTASQCQQPADNKLSDLLAPISEQIKEVITFREKN*GSKLFNHLSAVSESIQA

Parental  LGWVAMAPKPGPYVKEMND-AAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQAYIKEFHTTGLAWSK
          LGWVAMAPKPGPYVK.MND..AMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQA.IKEFHTT.LAW.K
Retrocopy LGWVAMAPKPGPYVK*MND<SAMFYTNRVLKEYKDVDKKHVDWVKAYLSIWTELQACIKEFHTTRLAWGK

Parental  TGPVAKELSGLPSGPSAGSGPPPPPPGPPPPPVSTSSGSDESASRSALFAQINQGESITHALKH-VSDDM
          TGPV.KELSGLPSGPSAGSGPPPPPPG.PPPPVSTSSGSDESAS.SALF.QINQGESITHALKH..SDDM
Retrocopy TGPVGKELSGLPSGPSAGSGPPPPPPGSPPPPVSTSSGSDESASHSALFVQINQGESITHALKH<LSDDM

Parental  KTHKNPALNAQSDPVRSGPKPFSAPKPQTSPSPKPATKKEPAVLELEGKKWRVENQENVSNLVIEDTELK
          KTHKNPAL.AQS.P.RSGPKPFSAPKPQTSPSPKPATKKEPA.LELEGKKWRVENQENVSNLVIEDTELK
Retrocopy KTHKNPALKAQSGPLRSGPKPFSAPKPQTSPSPKPATKKEPAILELEGKKWRVENQENVSNLVIEDTELK

Parental  QVAYIYKCVNTTLQIKGKINSITVDDCKKLGLVFDDVV
          QVAYIYKCVNTTLQIKGKI.SITVD..KKLGLVF.DVV
Retrocopy QVAYIYKCVNTTLQIKGKISSITVDNRKKLGLVFNDVV

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_1600 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 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,