RetrogeneDB ID: retro_nleu_1995

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397321.1:13276071..13277101(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: USP12
• Ensembl ID: ENSNLEG00000000323
• Aliases: None
• Description: None

Sequence

>retro_nleu_1995
AAAGAGATTGGTCCAGAACAGTTTCCAGTCAATGAGCATTATTTTGGATTAGTCAATTTTGGGAATACCTGCTACTGCAA
TTCAGTTCTTCAAGCACTTTATTTTTGTCGTCCATTTCGGGAAAAAGTTCTTGCATATAAGAGTCAACCTAGGAAAAAGG
AGAGCCTTCTTACATGCTTAGCAGATCTCTTCCACAGCATAGCCACTCACAAGAAAAAGTTTGGAGTAATACCTCCTAAG
AAGTTCATCACAAGATTACAGAAAGAAAATGAGCTTTTCGACAACTACATGAAACAAGATGCCCGTGAATTCTTAAATTA
CCTACTAAATACAATTGGTGATATTTTACAAGAAGAGAGAAAGCAGGAAAAACAAAATGGTTGCTAACCTAATGATAATA
TTGATAATGAAAATAATAACAGCACACCAGACCCAACGTGGGTTCATGAGATTTTTCAGGGAACATTAACTAATGAAACC
AGACGTCTTGTGAAACTATAAGCAGCAAAGATGAAGATTTTTTAGACCTTTCTGTTGACGTGGAACAAAATACATCAATT
ACTCACTGCTTAAGGGGTTTCAGCAACACAGAAACTCTATGCAGTGAATACAAGTATTACTGTGAAGAGCGTCGCAGCAA
ACAGGAAGCACACAAACGGATGAAAGTTTAAAAACTGCCCATGATTCTAGCTCTACACTTGAAGAGATTTAAATATATGG
ATCAACTTCATCCATATACAAAACTCTCTTACCGGGTAGTTTTTCCTTTAGAACTTCGTCTATTTAACACTTTAGGTGAT
GCCACCAATCCATACAGAATGTACGACCTTGTTGCTGTTGTGGTTCACTGTGGAAGTGGTCCCAGTTGAGGCCATTATAT
TGCAATAGTTAAGAGTCATGATTTTTGGTTGTTGTTTGATGACATTGTAGAAAAAATAGATGCACAAGCTATTGAAGAAT
TCTACGGGTTAACACCAGATACTCAAAGAACTCTGAGTCTGGTTACATACCTTTCTATCAGTCTCGGGAC

Alignment

ORF - retro_nleu_1995 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.57 %
• Parental protein coverage: 97.46 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKESLLTCLADLFHSIATQ
          KEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKESLLTCLADLFHSIAT.
Retrocopy KEIGPEQFPVNEHYFGLVNFGNTCYCNSVLQALYFCRPFREKVLAYKSQPRKKESLLTCLADLFHSIATH

Parental  KKKVGVIPPKKFITRLRKENELFDNYMQQDAHEFLNYLLNTIADILQEERKQEKQNGRLPNGNIDNENNN
          KKK.GVIPPKKFITRL.KENELFDNYM.QDA.EFLNYLLNTI.DILQEERKQEKQNG..PN.NIDNENNN
Retrocopy KKKFGVIPPKKFITRLQKENELFDNYMKQDAREFLNYLLNTIGDILQEERKQEKQNGC*PNDNIDNENNN

Parental  STPDPTWVHEI-FQGTLT--NETRCLTCETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETLCSEYKY
          STPDPTWVHEI.F.G.....N.T....CETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETLCSEYKY
Retrocopy STPDPTWVHEI<FSGNIN**NQT---SCETISSKDEDFLDLSVDVEQNTSITHCLRGFSNTETLCSEYKY

Parental  YCEECRSKQEAHKRMKVKKLPMILALHLKRFKYMDQLHRYTKLSYRVVFPLELRLFNTSGDATNPDRMYD
          YCEE.RSKQEAHKRMKV.KLPMILALHLKRFKYMDQLH.YTKLSYRVVFPLELRLFNT.GDATNP.RMYD
Retrocopy YCEERRSKQEAHKRMKV*KLPMILALHLKRFKYMDQLHPYTKLSYRVVFPLELRLFNTLGDATNPYRMYD

Parental  LVAVVVHCGSGPNRGHYIAIVKSHDFWLLFDDDIVEKIDAQAIEEFYGLTSD-ISKNSESGYILFYQSRD
          LVAVVVHCGSGP..GHYIAIVKSHDFWLLF.DDIVEKIDAQAIEEFYGLT.D..SKNSESGYI.FYQSRD
Retrocopy LVAVVVHCGSGPS*GHYIAIVKSHDFWLLF-DDIVEKIDAQAIEEFYGLTPD<YSKNSESGYIPFYQSRD

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_1995 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 9 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000019344	5 retrocopies	retro_cjac_2734, retro_cjac_3901, retro_cjac_3964, retro_cjac_3965, retro_cjac_4011,
Homo sapiens	ENSG00000152484	4 retrocopies	retro_hsap_2328, retro_hsap_3266, retro_hsap_4726, retro_hsap_4918,
Microcebus murinus	ENSMICG00000006269	2 retrocopies	retro_mmur_1167, retro_mmur_1187,
Macaca mulatta	ENSMMUG00000021425	1 retrocopy	retro_mmul_937,
Nomascus leucogenys	ENSNLEG00000000323	3 retrocopies	retro_nleu_1817, retro_nleu_1995 , retro_nleu_2426,
Otolemur garnettii	ENSOGAG00000030639	1 retrocopy	retro_ogar_2897,
Pongo abelii	ENSPPYG00000005232	3 retrocopies	retro_pabe_2110, retro_pabe_2705, retro_pabe_3672,
Pan troglodytes	ENSPTRG00000005727	3 retrocopies	retro_ptro_1701, retro_ptro_2209, retro_ptro_3143,
Tupaia belangeri	ENSTBEG00000012960	2 retrocopies	retro_tbel_3285, retro_tbel_4692,