RetrogeneDB ID: retro_nleu_2362

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397348.1:2689276..2690383(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHC1
• Ensembl ID: ENSNLEG00000011515
• Aliases: None
• Description: None

Sequence

>retro_nleu_2362
TGTGCCAGGTGCCAAGGGGCGGGGGGGACAGGGAGGAGAAAGCCCTGTAGCCATCCACTCAGCTCTATCCTGGGAAGGAG
TAACCTGAAATTTGCTGGAATGATAATCACTGTCACCATCTCCACCAGCAGCCTCAACGTCATGGTTGCAGACTGCAAAC
ATTATCACTAACCATCATATGCAATCTATCTCATTTGCATCCAGTGGGGATCCGGACACAGCCGAGTATGTCACCAACAT
TGCCAAAGACCCTGTGAATCAGAAGGCCTGCCACATTCTGGAGTGTCCTCAAGGGCTTGCCCAGGATGTCATCAGCACCA
CTGGCCAGCCTTCGACTTGCACTTTAAACAATGCCTCAGGAAACCACCCAAACTCGTCACCCCCTATGACAGGATGACTG
GCTTTGATGGCTTAGCTTGGGATGAGGAGGAGGGAGAGCCGCCTGGCCATCAGCACTATAATGACTTCCTGGGAAGGGAC
CCCCTCTTTGGCATGTGGTATACATGAGGCTTCGGGAAGGAGCCGCTCCAGGAGCTGCTCGACCCACTCCACCAAGTGCC
CAGACCCCCAGCCACTTGGGAGCTACACTGCCTTTAGGACAGTCTGTTGGGGGAGATCCAGAAGTTTGCAAACAGATGCC
ACCTCCCCCACCCTGTCTAGCCAGAGAGCTCTTTGATGATCCCTCCAATGTCAACATGCAGAACCTAGACAAGTCCTGGC
AAGCAGGGGGTGGTGCTGGGACCCCCAATCCTGCCATCAATGGCAGCACACCCTGGGATCTGTTTGACATGAAGCCCTTT
GAAGATGCTCTTCACATGCCTCCTCCTCCCCAGTTGGTGTCCATGGCTGAGCAGCTCTGAGGGGACCCCTGGTTCCATGG
GAAGCTGAGCTAGCGGGAGGCTGAGGCACTGCTGCAGCTCAACGGGGACTTCCTGGTGCAGGAGAGCATGACCACACCTG
GCCAGTATGTGCTCACTGGCTTGCAGAGTGGGGACCCCAAGCATCTGCTACTGGTGGACCCTGAGGGTGTAGTTCGGACA
AAGGATCACCGCTTTGAGAGTGTCAGTCACCTCATCAGCTACCACATGGACAATCACTTGCCCATCA

Alignment

ORF - retro_nleu_2362 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.86 %
• Parental protein coverage: 80.69 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  CEAVPGAKGATRRRKPCSRPLSSILGRSNLKFAGMPITLTVSTSSLNLMAADCKQ-IIANHHMQSISFAS
          C....GA.G.T.RRKPCS.PLSSILGRSNLKFAGM.IT.T.STSSLN.M.ADCK..I...H.MQSISFAS
Retrocopy CARCQGA-GGTGRRKPCSHPLSSILGRSNLKFAGMIITVTISTSSLNVMVADCKH>ITNHH-MQSISFAS

Parental  GGDPDTAEYVAYVAKDPVNQRACHILECPEGLAQDVISTIGQ-AFELRFKQYLRNPPKLVTPHDRMAGFD
          .GDPDTAEYV...AKDPVNQ.ACHILECP.GLAQDVIST.GQ.AF.L.FKQ.LR.PPKLVTP.DRM.GFD
Retrocopy SGDPDTAEYVTNIAKDPVNQKACHILECPQGLAQDVISTTGQ<AFDLHFKQCLRKPPKLVTPYDRMTGFD

Parental  GSAWDEEEEEPPDHQYYNDF-PGKEPPLGGVVDMRLREGATPGAARPTVPTAQTPSHLGATLPVGQPVGG
          G.AWDEEE.EPP.HQ.YNDF.PGK.PPL..VV.MRLREGA.PGAARPT.P.AQTPSHLGATLP.GQ.VGG
Retrocopy GLAWDEEEGEPPGHQHYNDF<PGKGPPLWHVVYMRLREGAAPGAARPTPPSAQTPSHLGATLPLGQSVGG

Parental  DPEVRKQMPPPPPCPAGRELFDDPSYVNVQNLDKARQAVGGAGPPNPAVNGSAPRDLFDMKPFEDALRVP
          DPEV.KQMPPPPPC.A.RELFDDPS.VN.QNLDK..QA.GGAG.PNPA.NGS.P.DLFDMKPFEDAL..P
Retrocopy DPEVCKQMPPPPPCLA-RELFDDPSNVNMQNLDKSWQAGGGAGTPNPAINGSTPWDLFDMKPFEDALHMP

Parental  PPPQSVSMAEQLRGEPWFHGKLSRREAEALLQLNGDFLVRESTTTPGQYVLTGLQSGQPKHLLLVDPEGV
          PPPQ.VSMAEQL.G.PWFHGKLS.REAEALLQLNGDFLV.ES.TTPGQYVLTGLQSG.PKHLLLVDPEGV
Retrocopy PPPQLVSMAEQL*GDPWFHGKLS*REAEALLQLNGDFLVQESMTTPGQYVLTGLQSGDPKHLLLVDPEGV

Parental  VSVAE-VWVRVAERKYSTLQCIRVPS
          V........RV......T...I..PS
Retrocopy VRTKD>TALRVSVTSSATTWTITCPS

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_2362 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009236	1 retrocopy	retro_cjac_2573,
Homo sapiens	ENSG00000160691	1 retrocopy	retro_hsap_4690,
Nomascus leucogenys	ENSNLEG00000011515	1 retrocopy	retro_nleu_2362 ,
Pongo abelii	ENSPPYG00000000769	1 retrocopy	retro_pabe_3643,
Pan troglodytes	ENSPTRG00000001397	1 retrocopy	retro_ptro_3117,
Tarsius syrichta	ENSTSYG00000011380	1 retrocopy	retro_tsyr_1773,