RetrogeneDB ID: retro_nleu_106

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397386.1:4557395..4559090(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000019348
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSNLEG00000014052
• Aliases: None
• Description: Ubiquitin carboxyl-terminal hydrolase [Source:UniProtKB/TrEMBL;Acc:G1RV03]

Sequence

>retro_nleu_106
ATGCCCCAGGCCTCTGAGCACCGCCTGGGCCGGACCCGAGAGCCACCTGTTAATATCCAGCCCCGAGTGGGATCCAAGCT
ACCATTTGCCCCCAGGGCCCGCAGCAAGGAGCGCAGAAACCCAGCCTCTGGGCCAAACCCCATGTTACGACCTCTGCCTC
CCCGGCCAGGTCCTCCTGATGAACGGCTCAAGAAACTGGAGCTGGGACGGGGACGGACCTCAGGCCCTCGTCCCAGAGGC
CCCCTTCGAGCAGATCATGGGGTTCCCCTGCCTGGCTCACCACCCCCAACTGTGGCTTTGCCTCTCTCATCTCGGACCAA
CTTAGCCCGTTCCAAGTCTGTGAGCAGTGGGGACTTGCGTCCAATGGGGATTGCCTTGGGAGGGCACTGTGGCACCGGAG
AGCTTGGGGCTGCACTGAGCTGCTTGGCCCTCCGGCCTGAGCCACCCACTTTGAGACGTAGCACTTCTCTCCGCCGCCTA
GGGGGCTTTCCTGGACCCCCTACCCTGTTCAGCATACGGACACAGCCCCCTGCTTCCCATGGCTCCTTCCACATGATATC
CGCCCGGTCCTCTGAGCCTTTCTACTCTGATGACAAGATGGCTCATCACACACTGCTTCTGGGCTCTGGTCATGTTGGCC
TTCGAAACCTGGGAAACACGTGCTTCCTGAATGCTGTGCTGCAGTGTCTGAGCAGCACTCGACCTCTTCGGGACTTCTGT
CTGAGAAGGGACTTCTGGCAAGAGGTGCCTGGAGGAGGCCGAGCCCAAGAGCTCACTGAAGCCTTTGCAGATGTGACTGG
TGCCCTCTGGCACCCTGACTCCTGCGAAGCTGTGAATCCTACTCGATTCCGAGCTGTCTTCCAGAAATATGTTCCCTCCT
TCTCTGGATACAGCCAGCAGGATGCCCAAGAGTTCCTGAAGCTCCTCATGGAGCGGCTACACCTTGAAATCAACCGCCGA
GGCCGCCGGGCTCCACCAATACTTGCCAATGGTCCGGTTCCCTCTCCACCCCGCCGAGGAGGGGCTCTGCTAGAAGAACC
TGAGTTCAGTGATGATGACCGAGCCAACCTAATGTGGAAACGTTACCTGGAGCGAGAGGACAGCAAGACTGTGGACCTGT
TTGTGGGCCAGTTGAAAAGTTGTCTCAAGTGCCAGGCCTGTGGGTATCGCTCCACGACCTTCGAGGTTTTTTGTGACCTG
TCCCTGCCCATCCCCAAGAAAGGATTTGCTGGGGGCAAGGTGTCTCTGCGGGATTGTTTCAACCTTTTCCCTAAGGAAGA
AGAGCTAGAGTCGGAGAATGCCCCAGTGTGTGACCGATGTCGGCAGAAAACTCGAAGTACCAAAAAGTTGACAGTACAAA
GATTCCCTCGAATCCTCGTGCTCCATCTGAATCGATTTTCTGCCTCCCGAGGCTCCATCAAAAAAAGTTCAGTAGGTGTA
GACCTTCCACTGCAGCGACTGAGCCTAGGGGACTTTGCCAGTGACAAAGCCGGAAGTCCTGTATACCAGCTGTATGCCCT
TTGCAACCACTCAGGCAGCGCCCACTATGGCCACTACACAGCCCTGTGCCGGTGCCAGACTGGTTGGCATGTCTACAATG
ACTCTCGTGTCTCCCCTGTCAGTGAAAACCAGGTGGCATCCAGCGAGGGCTACGTGCCGTTCTACCAACCGATGCAGGAG
CCACCCCGGTGCCTG

Alignment

ORF - retro_nleu_106 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.51 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPQASEHRLGRTREPPVNIQARVGSKLPFAPRARSKERRNPASGPNPMLRPLPPRPGPPDERLKKLELGR
          MPQASEHRLGRTREPPVNIQ.RVGSKLPFAPRARSKERRNPASGPNPMLRPLPPRPGPPDERLKKLELGR
Retrocopy MPQASEHRLGRTREPPVNIQPRVGSKLPFAPRARSKERRNPASGPNPMLRPLPPRPGPPDERLKKLELGR

Parental  GRTSGPRPRGPLRADHGVPLPGSPPPAVALPLPSRTNLARSKSVSSGDLRPMGIALGGHRGTGELGAALS
          GRTSGPRPRGPLRADHGVPLPGSPPP.VALPL.SRTNLARSKSVSSGDLRPMGIALGGH.GTGELGAALS
Retrocopy GRTSGPRPRGPLRADHGVPLPGSPPPTVALPLSSRTNLARSKSVSSGDLRPMGIALGGHCGTGELGAALS

Parental  RLALRPEPPTLRRSTSLRRLGGFPGPPTLFSIRTEPPASHGSFHMISARSSEPFYSDDKMAHHTLLLGSG
          .LALRPEPPTLRRSTSLRRLGGFPGPPTLFSIRT.PPASHGSFHMISARSSEPFYSDDKMAHHTLLLGSG
Retrocopy CLALRPEPPTLRRSTSLRRLGGFPGPPTLFSIRTQPPASHGSFHMISARSSEPFYSDDKMAHHTLLLGSG

Parental  HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFRQEVPGGGRAQELTEAFADVIGALWHPDSCEAVNP
          HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDF.QEVPGGGRAQELTEAFADV.GALWHPDSCEAVNP
Retrocopy HVGLRNLGNTCFLNAVLQCLSSTRPLRDFCLRRDFWQEVPGGGRAQELTEAFADVTGALWHPDSCEAVNP

Parental  TRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANGSVVFLLSHGCSLLPLICGS
          TRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANG.V......G..LL.....S
Retrocopy TRFRAVFQKYVPSFSGYSQQDAQEFLKLLMERLHLEINRRGRRAPPILANGPVPSPPRRGGALLEEPEFS

Parental  DDDRANLMWKRYLEREDSKIVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCF
          DDDRANLMWKRYLEREDSK.VDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCF
Retrocopy DDDRANLMWKRYLEREDSKTVDLFVGQLKSCLKCQACGYRSTTFEVFCDLSLPIPKKGFAGGKVSLRDCF

Parental  NLFTKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILGLDLNRFSASRGSIKKSSVGVDFPLQRLSLG
          NLF.KEEELESENAPVCDRCRQKTRSTKKLTVQRFPRIL.L.LNRFSASRGSIKKSSVGVD.PLQRLSLG
Retrocopy NLFPKEEELESENAPVCDRCRQKTRSTKKLTVQRFPRILVLHLNRFSASRGSIKKSSVGVDLPLQRLSLG

Parental  DFASDKAGDPVYQLYALCNHSGSVHYGHYTALCRCQTGWHVYNDSRVSPVSENQVASSEGYVLFYQLMQE
          DFASDKAG.PVYQLYALCNHSGS.HYGHYTALCRCQTGWHVYNDSRVSPVSENQVASSEGYV.FYQ.MQE
Retrocopy DFASDKAGSPVYQLYALCNHSGSAHYGHYTALCRCQTGWHVYNDSRVSPVSENQVASSEGYVPFYQPMQE

Parental  PPRCL
          PPRCL
Retrocopy PPRCL

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_106 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000016189	1 retrocopy	retro_ecab_260,
Nomascus leucogenys	ENSNLEG00000014052	1 retrocopy	retro_nleu_106 ,