RetrogeneDB ID: retro_nleu_2027

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397323.1:3708196..3709871(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TOX4
• Ensembl ID: ENSNLEG00000014556
• Aliases: None
• Description: None

Sequence

>retro_nleu_2027
ATGGAGTTTCCCGGAGGAAATGACAATTACCTGACAATCACAGGGCCTTCACACCCCTTCCTGTCAGGGGCCAAGACATT
CCATATACCAAGCTTGGGTGAGGAGGAATTTGAAATCCTACCCATCTCCTTGGATTCTGATCCCTCATTGGCTGTCTCAG
ATGTGGTTGACCACTTTGACGACCTGGCAGACCCTTCCTCTTCACAGGATGGCAGTTCTTCAGCCCAGTATGGGGTCCAG
ACATTGGACATGCTCTGTGGGCATGACTCATGGCTTGATGGAGCAAGGCGGGGGCTCCTCGGTGGAGGCTTGATCATGGA
CTTGAACCACTCTATAGGAACTCAGTATAGTGCCAACCCACCTGTTACAATTGATGTACTAATGATGGACATAACATCTG
GCTTGATGGGGCATCGCCAGTTGACCACCATTGATCAGTCAGAACTGAGTTTCCAACTGGGTTTGAGCTTAGGGGGTGGC
ACCATCCTGCCACCTGCCCAGTCACCTGAAGATCGTCTTTCAACCATGCCCTCACCTCCTAGTTCACTTCACGAGGATGG
TGTTGAGGATTTCCGGAGGCAAATTTCCAGCCAGAAGACAGTGGTGGTGGAAGCAGGGAAAAAGCAGAAGGTCCCAAAGA
AGAGAAAAAAGAAAGATCCTAATGAACCTCAGAAACAGTTTCAGCATATGCTTTATTATTTTGTGATACACAGGCTGCCA
TCAAGGGACAGAATCCTAATGCCACTTTTGGTGAGGTTTCAAAAATTGTGGCCTCCATGTGGGATAGTCTTAGGAGCAAA
AACAGATATATAAGAGGAAAACTGAGGCTGCCAAGAAAGAGTATCTGAAGGCACTGGCTGCTTACAAAGACAACCAGGAG
TGTCAGGCCACTGTGGAAACAGCGGAATTGGATCCAGCACCACCATCACAAACTCCTTCTCCACCTCCTATGGCTACTGT
TGACCCAGCATCTCCAGCACCAGCTTCAACAAAGCCCCCTGTCCTGTCCCCATCCATTGTTGTTAACTCCACCCTTTCAT
CCTATGTGGCAAACCAGGCATCTTCAGGAGCTGGGGGTCAGCCCAGTATCACCAAGTTGATTATTACCAAACAAACGTTG
CCCTCTTCCATTACTATATCTCAAGGAGGGATGGTTACTGCTATCCCAGCCACAGTGGTGACCTCCTGGGGGCTCCAACT
AGGCCAAACCAGTACAGCTACTATCCAGTCCAGCCAACAAGCCCAGATTGTCACTCAGTTAGTGCTGCACGCAGCAGCAG
CAGCTGCTGCTGTTGCTTCTATGCAACTGCCTCCACCCCGACTACAGCCCCCTCCATTACAACAGATGCCACAGCCCCCG
ACTCAGCAGCAAGTTACCATTCTGCAGCAGCCTCCTCCACTCCAGGCCATGCAACAGCCTCCACCTCAGAAAGTTCGAAT
CAATTTACAGCACATCAAGAATGTGCCTCCACTCACTTTGAAAATGCAGACTACCTTAGTCCTACCAACTGCGGAAAGTA
GTCCTGAGCGGCCTATGAACAATAGCCCTGAGACCCATACAGTGGAAGCAACTTCTCCTGAGACTATCTGTGAGATGATC
ACAGATGTAGTTCATGAGGTTGAGTCTCCTTATGAGATGGATGTTGAATTGGTGAGTGGGTTTCCTGTGGCACTC

Alignment

ORF - retro_nleu_2027 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.43 %
• Parental protein coverage: 89.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEFPGGNDNYLTITGPSHPFLSGAETFHTPSLGDEEFEIPPISLDSDPSLAVSDVVGHFDDLADPSSSQD
          MEFPGGNDNYLTITGPSHPFLSGA.TFH.PSLG.EEFEI.PISLDSDPSLAVSDVV.HFDDLADPSSSQD
Retrocopy MEFPGGNDNYLTITGPSHPFLSGAKTFHIPSLGEEEFEILPISLDSDPSLAVSDVVDHFDDLADPSSSQD

Parental  GSFSAQYGVQTLDM-PVGMTHGLMEQGG-GLLSGGLTMDLDHSIGTQYSANPPVTIDVPMTDMTSGLMGH
          GS.SAQYGVQTLDM..VGMTHGLMEQGG.GLL.GGL.MDL.HSIGTQYSANPPVTIDV.M.D.TSGLMGH
Retrocopy GSSSAQYGVQTLDM>SVGMTHGLMEQGG<GLLGGGLIMDLNHSIGTQYSANPPVTIDVLMMDITSGLMGH

Parental  SQLTTIDQSELSSQLGLSLGGGTILPPAQSPEDRLSTTPSPTSSLHEDGVEDFRRQLPSQKTVVVEAGKK
          .QLTTIDQSELS.QLGLSLGGGTILPPAQSPEDRLST.PSP.SSLHEDGVEDFRRQ..SQKTVVVEAGKK
Retrocopy RQLTTIDQSELSFQLGLSLGGGTILPPAQSPEDRLSTMPSPPSSLHEDGVEDFRRQISSQKTVVVEAGKK

Parental  QKAPKKRKKKDPNEPQK-PVSAYALFFRDTQAAIKGQNPNATFGEVSKIVASMWDSLGEEQKQVYKRKTE
          QK.PKKRKKKDPNEPQK..VSAYAL.F.DTQAAIKGQNPNATFGEVSKIVASMWDSL..........K..
Retrocopy QKVPKKRKKKDPNEPQK<TVSAYALLFCDTQAAIKGQNPNATFGEVSKIVASMWDSLRSKNRYI-RGKLR

Parental  AAKK-EYLKALAAYKDNQECQATVETVELDPAPPSQTPSPPPMATVDPASPAPASIEPPALSPSIVVNST
          ...K.EYLKALAAYKDNQECQATVET.ELDPAPPSQTPSPPPMATVDPASPAPAS..PP.LSPSIVVNST
Retrocopy LPRK<EYLKALAAYKDNQECQATVETAELDPAPPSQTPSPPPMATVDPASPAPASTKPPVLSPSIVVNST

Parental  LSSYVANQASSGAGGQPNITKLIITKQMLPSSITMSQGGMVTVIPATVVTSRGLQLGQTSTATIQPSQQA
          LSSYVANQASSGAGGQP.ITKLIITKQ.LPSSIT.SQGGMVT.IPATVVTS.GLQLGQTSTATIQ.SQQA
Retrocopy LSSYVANQASSGAGGQPSITKLIITKQTLPSSITISQGGMVTAIPATVVTSWGLQLGQTSTATIQSSQQA

Parental  QIVTRSVLQAAAAAAAAASMQLPPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQ-
          QIVT..VL.AAAAAAA.ASMQLPPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQ.
Retrocopy QIVTQLVLHAAAAAAAVASMQLPPPRLQPPPLQQMPQPPTQQQVTILQQPPPLQAMQQPPPQKVRINLQH

Parental  -QQPPPLQIKSVPLPTLKMQTTLVPPTVESSPERPMNNSPEAHTVEATSPETICEMITDVVPEVESPSQM
          ....PPL..K......L.............SPE..........T..........E........VE..S..
Retrocopy IKNVPPLTLKMQTTLVLPTAESSPERPMNNSPETHTVEATSPETICEMITDVVHEVESPYEMDVELVSGF

Parental  DVEL
          .V.L
Retrocopy PVAL

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_2027 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006261	1 retrocopy	retro_amel_858,
Canis familiaris	ENSCAFG00000005647	2 retrocopies	retro_cfam_1625, retro_cfam_1698,
Choloepus hoffmanni	ENSCHOG00000000714	2 retrocopies	retro_chof_2239, retro_chof_631,
Homo sapiens	ENSG00000092203	1 retrocopy	retro_hsap_2970,
Macropus eugenii	ENSMEUG00000010501	1 retrocopy	retro_meug_1384,
Mustela putorius furo	ENSMPUG00000000181	1 retrocopy	retro_mputfur_718,
Mus musculus	ENSMUSG00000016831	1 retrocopy	retro_mmus_11,
Nomascus leucogenys	ENSNLEG00000014556	1 retrocopy	retro_nleu_2027 ,
Pongo abelii	ENSPPYG00000005598	1 retrocopy	retro_pabe_2463,
Pan troglodytes	ENSPTRG00000006126	1 retrocopy	retro_ptro_2008,
Sus scrofa	ENSSSCG00000029203	1 retrocopy	retro_sscr_361,