RetrogeneDB ID: retro_nleu_840

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397274.1:11940890..11942728(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM35A
• Ensembl ID: ENSNLEG00000011652
• Aliases: None
• Description: family with sequence similarity 35, member A [Source:HGNC Symbol;Acc:28773]

Sequence

>retro_nleu_840
CAGCTTTTATACAGTCAACATTCTTTATATCTGAAGGATGAAAAACAGCACAAAAATCTTGAAAACTATGAAGTCCCAGA
ATCTATTGGTCCTCCAGATCTTAGTGGTCATTTCTTAGCAAACTGTATGAATAGACATGTTCATGTGAAAGATGACTTTG
TACATTCTGTTTCTGAAACACAGAATATAGAATCCCAGAAGATTCACTCCTCTAGACTGAGTAATATAACTAGCTCTAAT
ATGCAAATATGTGGATTTAAAAGCACAGTTCCGCATTTAACCAAAGAAGAAAAGTATCAAAAGCTTCTCAGTGAAAATAA
AATTATAGATGAACAGCCTAAACATCAGTCAGATATATGTGGTCAGAACTTTAACGCAAGTTTGTTTCAGCTAGGCCATA
AATGTGCAGCTATGTTGGATTTGGTTTGTAGTGCTGAACAAATTAATATAGGGCCTGAAGTGGTACAAACAGAGTGTGTG
CCAGCGGAATATCATGAAATACAAAACCAGTGTTTGGGATTATTTTCCTCGAACGCAGTAGATAAGTCAAGGTCTGAAGC
AGCAGTTAGGAAGGTCTCAGACCTTAAAATATCAACTGATACAGAATTTCTCAGTATAATTACCTCCAGCCAGGTTGCTT
TTTTAGCTCAAAAGAAAGATAAAGGGCGGAGTCCTATAAATAAAGGGAATGTAAACATGGAGGCTGAACCAAAGGCAAGT
TATGGGGAGATAAGAATACCTGAAGAGAATTCGATTCAGCTTGATGGTTTTACAGAAGCATATGAAAGTGGACAAAACCA
AGCATATTCCCTTGAACTTTTTAGTCCTGTTTGTCCTAAAACAGAAAATAGCCGCATTCACATAAACTCTGATAAAGGTC
TTGAAGAACATACAGGATCTCAAGAACTTTTCAGTTCTGAAGATGAACTGCCACCAAATGAGATACGTATTGAGTTGTGT
AGCTCAGGAATATGTGTTCCCAACTAAATACCTTCCACAAAAGTGCTATTAAAAGAAGCTGCACCTCTGAAGATAAAGTG
GGCCAGTCTGAAGCTCTATCTAGAGTCCTTCAAGTAGCTAAGAAAATGAAGTTGATTTCTAATGGAGGAGATTCTGCTGT
AGAAATGGATCGGAGGAATGTGTCTGAATTTAAGGGTATTAAAAAAACATCATTAATAAAAAACTGTGATTTTAAAAGCC
AGAAGTATAATTGTTTAGTCATGGTGCTATCTCCATGCCATGCGAAGGAAATAAACATAAAATTTGGACCAAATTCTGGC
TCTAAAGTGCCTTTAGCAACAGTTACAGTAATTGATCAATCAGAAACTAAGAAGAAGGTTTTCTGTGGAGGACTGCAGCA
TTTTGGGCATTTACAGTGCTTCTTGGAGATATAATTTTACTCACAGATGTTGTTATTCATGAGGACCAATGGGTTGGTGA
GACAGTACTACAATCAACATTTAGCAGTCAGTTATTAAATCTTGGGAGTTATTCATCTATTCAGCCTGAAGAATATTCCA
GTGTAGTTAGTGACGTTGTACTTCAAGACTTACTGGCATATGTGTCCTCAAAACATTCCTACCTCAGAAATCTTCCTCCG
AGGCAGCCTCAGAGGGTGAACAGTATAGACTTTGTAGAATTGGAGCACCTTCAACCTGATGTATTAGTCCACGCAGTACT
AAGAGTTGTTGATTTCACTATACTGACAGAGGCAGTATACAGTTATAGAAGACAGAAGCAGAAAAAAGTTAACAGTGGAA
GAGGCCCAAGATCAACATTATGTGCTTGTATTATGGGGTCCTGGAGCAGCCTGGTACCCTCAACTTCAAAGGAAAAAA

Alignment

ORF - retro_nleu_840 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.66 %
• Parental protein coverage: 68.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QLLYSQHSLYLKDEKQHKNLENYEVPESIGSPDVSGHFLANCMNRHVHVKDDFVRSVSETQNIESQKIHS
          QLLYSQHSLYLKDEKQHKNLENYEVPESIG.PD.SGHFLANCMNRHVHVKDDFV.SVSETQNIESQKIHS
Retrocopy QLLYSQHSLYLKDEKQHKNLENYEVPESIGPPDLSGHFLANCMNRHVHVKDDFVHSVSETQNIESQKIHS

Parental  SRLSDITSSNMQICGFKSTVPHLAKEEKDQKLLSENKIIDEQPKHQADICGQNFNTDLFQLGHKCAAILD
          SRLS.ITSSNMQICGFKSTVPHL.KEEK.QKLLSENKIIDEQPKHQ.DICGQNFN..LFQLGHKCAA.LD
Retrocopy SRLSNITSSNMQICGFKSTVPHLTKEEKYQKLLSENKIIDEQPKHQSDICGQNFNASLFQLGHKCAAMLD

Parental  LVCSTEQINIGPEVVQRECVPTEYHEIQNQCLGLFSSNAVDNSRSEAAVRKVSDLKISTDTEFLSIITSS
          LVCS.EQINIGPEVVQ.ECVP.EYHEIQNQCLGLFSSNAVD.SRSEAAVRKVSDLKISTDTEFLSIITSS
Retrocopy LVCSAEQINIGPEVVQTECVPAEYHEIQNQCLGLFSSNAVDKSRSEAAVRKVSDLKISTDTEFLSIITSS

Parental  QVAFLAQKKDKGRSPINKGNVNMEAEPKASYGEIRIPDENSIQLDGFTEAYESGQNQAYSLELFSPVCPK
          QVAFLAQKKDKGRSPINKGNVNMEAEPKASYGEIRIP.ENSIQLDGFTEAYESGQNQAYSLELFSPVCPK
Retrocopy QVAFLAQKKDKGRSPINKGNVNMEAEPKASYGEIRIPEENSIQLDGFTEAYESGQNQAYSLELFSPVCPK

Parental  TENSCIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGI-LCSQLNTFHKSAIKRSCTSEDKVGQ
          TENS.IHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGI..CSQLNTFHKSAIKRSCTSEDKVGQ
Retrocopy TENSRIHINSDKGLEEHTGSQELFSSEDELPPNEIRIELCSSGI<MCSQLNTFHKSAIKRSCTSEDKVGQ

Parental  SEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKTSLIKNCDSKSQKYNCLVMVLSPCHVKEIN
          SEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKTSLIKNCD.KSQKYNCLVMVLSPCH.KEIN
Retrocopy SEALSRVLQVAKKMKLISNGGDSAVEMDRRNVSEFKGIKKTSLIKNCDFKSQKYNCLVMVLSPCHAKEIN

Parental  IKCGRNSGSKVPLATVTVIDESETKKKVF-LWRTAAFWAFTVFLGDIILLTDVVIHEDQWVGETVLQSTF
          IK.G.NSGSKVPLATVTVID.SETKKKVF.LWRTAAFWAFTV.LGDIILLTDVVIHEDQWVGETVLQSTF
Retrocopy IKFGPNSGSKVPLATVTVIDQSETKKKVF<LWRTAAFWAFTVLLGDIILLTDVVIHEDQWVGETVLQSTF

Parental  STQLLNLGSYSSIQPEECSSVVSDVVLQDLLAYVSSKHSYLRDLPPRQPQRVNSIDFVELEHLQPDVLVH
          S.QLLNLGSYSSIQPEE.SSVVSDVVLQDLLAYVSSKHSYLR.LPPRQPQRVNSIDFVELEHLQPDVLVH
Retrocopy SSQLLNLGSYSSIQPEEYSSVVSDVVLQDLLAYVSSKHSYLRNLPPRQPQRVNSIDFVELEHLQPDVLVH

Parental  AVLRVVDFTILTEAVYSYRGQKQ-KKVMLTVEQAQDQHYVLVLWGPGAAWYPQLQRKK
          AVLRVVDFTILTEAVYSYR.QKQ.KK..LTVE.AQDQHYVLVLWGPGAAWYPQLQRKK
Retrocopy AVLRVVDFTILTEAVYSYRRQKQ>KK--LTVEEAQDQHYVLVLWGPGAAWYPQLQRKK

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_840 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000017	1 retrocopy	retro_dnov_2237,
Homo sapiens	ENSG00000122376	1 retrocopy	retro_hsap_1370,
Nomascus leucogenys	ENSNLEG00000011652	3 retrocopies	retro_nleu_1073, retro_nleu_2157, retro_nleu_840 ,
Pongo abelii	ENSPPYG00000002828	1 retrocopy	retro_pabe_1137,
Pan troglodytes	ENSPTRG00000002465	1 retrocopy	retro_ptro_941,