RetrogeneDB ID: retro_nleu_2939

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397497.1:245755..246922(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAPCD2
• Ensembl ID: ENSNLEG00000008908
• Aliases: None
• Description: None

Sequence

>retro_nleu_2939
ATGGCCCGGGCCCCGACGGCCCAGCGGAGCCTCATGCCTCCTGCCGCGCCCGCGCGCAGCACAGAGGGGCTGCTGCGCGC
CTTCCTGCAGAGCCTGCGCACGCTATTCCACATCCTGTACGATCCGCGGCGCGGCTGCGAGCACCTGCGAGAGATCCAGT
CCCGCTGGCAGGGCGCCGACGCGCGGGAGCTGCCCCTCGGGGTCCTGGAGGGCCTGCGCGAGGTGGCCCCTGCCAGCGGC
TACCTGACCTTCCAGCGCTTCGTGGCCGGCCTGCGCACCGCACTGCTGAGGCCGACGGCGGCCCCCGGGACCCCACGCAC
GCCCCGGCCCGGCCCAGGAACCAGCCGCCGCAGCGCCTGCTGTTCGCGCCGGCCGACGAGCCGCGGATGGTTCTGGAGAG
GAAGCACCTGCCCCTGGGCGAGCGCGCTTCTCTGGCTGGTCCCAGCCGCGCGGCCCGCAGCCCAGAGCAGCTGTGCGCCC
CCGCCGAGGCGGCGCTCTGCCCGGTGGAACCAGAGCGGTCCCAGAGCGCGGCGCTGGAACACAGCCCCAGCGCGGACGCA
GGTGCAGCGGCCTGCAGGGCTTGGAGCAGACTCAGGGGATGCCCCGCGGGCCCCCAGTGCCCGAGGAGACGTCAGAGGCA
CACCATCACCAGCGGCGTTGACTGCGGCCTGCTGAAGCAGATGAAGGAGCTAGAAGCAGGAGAAGGAGGTCCTGCTGCAG
GGTTTGGAGATGATGGCGCGGGGCCGCGATTGGTACCAGCAGCAGCTGCAACGAGTGCAGGAGCTCCAGTGCCGCCTGGG
CCAGAGCAGAGCCAGCGCCGACTTTGGGGCCACGGGGAGCCCCTGCCCACTGGGGCGGCTACTGTCCAAGGTACAGGAGG
TGGCCGGGTGCCTGGGGGAGCTGCTGGCTGCGGCCTGTGCCAGCTGGGCCCTGCCCACGTCCTCCTCCGGGCCCCCTGCT
CTGCCCTGAGGTCAACCTCGTCCCCGGGCTGTCAGCAGCAGACCATCCTCATGCTGAAGGAGCAGAACTGACTCCTTATC
CAGGAGGTGACCAAGAAGAGTGAGCGCATCACGCAGCTGGAGCAGAAGTCAGCGCTCATTAAGCAACTGTTTGAGGCCCG
CTCCCTGAGCCAGCAGGACAGGGGGGCCTCTGGACCCCACCTTCATC

Alignment

ORF - retro_nleu_2939 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.87 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MAGAAMAERGRVPPPAPAPSTEGLPRAFLQSLRTLFDILDDRRRGCVHLREIESRWQGTDARELPRGVLE
          MA.A..A.R...PP.APA.STEGL.RAFLQSLRTLF.IL.D.RRGC.HLREI.SRWQG.DARELP.GVLE
Retrocopy MARAPTAQRSLMPPAAPARSTEGLLRAFLQSLRTLFHILYDPRRGCEHLREIQSRWQGADARELPLGVLE

Parental  GLRQVAPASGYLTFERFVAGLRTSLL-SADGGPRDPTRAPARPGDQPPLPPQRLVFAPADEPRTVLERKP
          GLR.VAPASGYLTF.RFVAGLRT.LL..ADGGPRDPT.APARP..QPP...QRL.FAPADEPR.VLERK.
Retrocopy GLREVAPASGYLTFQRFVAGLRTALL<EADGGPRDPTHAPARPRNQPP---QRLLFAPADEPRMVLERKH

Parental  LPLGVRAPLADSSPAFRSTHSACAPACPPAAPASPRRLQRVAGEPGPCLSTTGAVACRA-LEADSADARR
          LPLG.RA.LA..S.A.RS....CAPA.....P..P.R.Q..A.E..P.....GA.ACRA.LE......R.
Retrocopy LPLGERASLAGPSRAARSPEQLCAPAEAALCPVEPERSQSAALEHSPS-ADAGAAACRA<LEQTQGMPRG

Parental  AP-RARGE-RRRHTITSGVDCGLLKQMKELE-QEKEVLLQGLEMMARGRDWYQQQLQRVQERQRRLGQSR
          .P..ARG..R.RHTITSGVDCGLLKQMKELE.QEKEVLLQGLEMMARGRDWYQQQLQRVQE.Q.RLGQSR
Retrocopy PP<SARGD<RQRHTITSGVDCGLLKQMKELE>QEKEVLLQGLEMMARGRDWYQQQLQRVQELQCRLGQSR

Parental  ASADFGAAGSPRPLGRLLPKVQEVARCLGELLAAACASRALPPSSSGP-PCPALTSTSPPGWQQQTILML
          ASADFGA.GSP.PLGRLL.KVQEVA.CLGELLAAACAS.ALP.SSSGP.PC.AL.STS.PG.QQQTILML
Retrocopy ASADFGATGSPCPLGRLLSKVQEVAGCLGELLAAACASWALPTSSSGP<PCSALRSTSSPGCQQQTILML

Parental  KEQNRLLTQEVTEKSERITQLEQEKSALIKQLFEARALNQQD-GGPLDSTFI
          KEQN.LL.QEVT.KSERITQLEQ.KSALIKQLFEAR.L.QQD.GGPLD.TFI
Retrocopy KEQN*LLIQEVTKKSERITQLEQ-KSALIKQLFEARSLSQQD>GGPLDPTFI

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_2939 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 5 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000186193	2 retrocopies	retro_hsap_3734, retro_hsap_3738,
Macaca mulatta	ENSMMUG00000007112	1 retrocopy	retro_mmul_1682,
Nomascus leucogenys	ENSNLEG00000008908	2 retrocopies	retro_nleu_2867, retro_nleu_2939 ,
Pongo abelii	ENSPPYG00000019804	5 retrocopies	retro_pabe_3124, retro_pabe_3222, retro_pabe_3223, retro_pabe_3233, retro_pabe_3527,
Pan troglodytes	ENSPTRG00000021589	6 retrocopies	retro_ptro_2530, retro_ptro_2532, retro_ptro_2534, retro_ptro_2537, retro_ptro_2543, retro_ptro_2992,