RetrogeneDB ID: retro_nleu_2291

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397342.1:152997..154159(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FKBP4
• Ensembl ID: ENSNLEG00000002835
• Aliases: None
• Description: FK506 binding protein 4, 59kDa [Source:HGNC Symbol;Acc:3720]

Sequence

>retro_nleu_2291
ATGCCCATGATTGGGGACTGAGCCTTTGTCCACTACACTGGCTGGCTGTTAGAGGGCACAAAGTTTAACTCCAGTCTGGA
TTGCAAGGACAAACTCTCCTTTGACCTGGGAAAAGGGGAGGTCATCAAGGCTTGGGACATTGCCATAGCAACTGTGAAGG
TGGGGGAGGTGTGCCACATCACCTGCAAACCAGAATATGCCTAGGGTTCAGCAGACAGTCCTCCAACGATCCCCCCACAA
TGCCACGCTTGTGTTTGAGGTGGAATTGTTTAAGGAAGAAGATCTGATGGAAGAGGAAGATGGGGGAATCATCCGCAGAA
TAGGGACTCACGGTGAAGGCTATGCCAAGCCCAATGAGGGCGCTATGGTGGAGGTTTCACTGGAAGGGTACTACAAGGAC
CAGCTCTTTGACCAACAGGAGCTTCGCTTTGAGGTTGGTGAGGGGGAGAACCTGGATCTGCCTTATGGTCTGGAGAGGGC
CATTCAGCACTTGGAGAAAGGAGAATATTCCACTGTGTACCTCAAGCCCAGCTATGCTTTTGGCAGTGTTGGGAAGGAAA
AGACCCAAATCCCGCCAAATGCCCAGCTGAAATATGAATTACACTTAAAGAGTTTGGAAAAGGCCAAGGACTCTTGGGAA
AAGAATTCAGAACAGAAGCTGGAACAGAACACTATAGTGAAAGAGCAGGGCAGTGTGTACTTCAAGGAAGGCAAATACAA
GCAAGCTTTACTACAGTGTAAGAAGATTGTGTCCTGGCTGGAATATGAGTCCAGTTTTTCCAGTGAGGAAGCACAGAAGT
CACAGGCCCTTCAACTGCCCTCTCCCCTCAACCTGGTCATGTGTCAGCTGAAACTACAGGCCTTCTCTGCTGCCATTGAA
AGCTGTAACAAGGCCCTAGAACTGGACAGCAACAACGAGAAGGGCCTCTTCTGCTGGGGAGAGGCCCACCTGGCGGTCAA
TGACTTTGAACTGGCTCGGGCTGACTTCCAGAAGGTCTTGCATCTCTGCCCCAACAATAAAGCGGCCGGGGCCCAGCTGG
CTGTGTGTCAGCAGCAGATCCGCAGGCAGCTTGCCCAGAAGAAGTAGCACTATGCCAACATGTTTGAGAGGCTGGCTGAG
GAGGAGAACAAGGCCAAGGCAGAGGCTTGCTCAGGAGACCAT

Alignment

ORF - retro_nleu_2291 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.9 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPMIGDRVFVHYTGWLLDGTKFDSSLDRKDKFSFDLGKGEVIKAWDIAIATMKVGEVCHITCKPEYAYGS
          MPMIGD..FVHYTGWLL.GTKF.SSLD.KDK.SFDLGKGEVIKAWDIAIAT.KVGEVCHITCKPEYA.GS
Retrocopy MPMIGD*AFVHYTGWLLEGTKFNSSLDCKDKLSFDLGKGEVIKAWDIAIATVKVGEVCHITCKPEYA*GS

Parental  AGSPPKIPP-NATLVFEVELFEFKGEDLTEEEDGGIIRRIQTRGEGYAKPNEGAIVEVALEGYYKDQLFD
          A.SPP.IPP.NATLVFEVELF..K.EDL.EEEDGGIIRRI.T.GEGYAKPNEGA.VEV.LEGYYKDQLFD
Retrocopy ADSPPTIPP>NATLVFEVELF--KEEDLMEEEDGGIIRRIGTHGEGYAKPNEGAMVEVSLEGYYKDQLFD

Parental  QRELRFEIGEGENLDLPYGLERAIQRMEKGEHSIVYLEPSYAFGSVGKEKFQIPPNAELKYELHLKSFEK
          Q.ELRFE.GEGENLDLPYGLERAIQ..EKGE.S.VYL.PSYAFGSVGKEK.QIPPNA.LKYELHLKS.EK
Retrocopy QQELRFEVGEGENLDLPYGLERAIQHLEKGEYSTVYLKPSYAFGSVGKEKTQIPPNAQLKYELHLKSLEK

Parental  AKESWEMNSEEKLEQSTIVKERGTVYFKEGKYKQALLQYKKIVSWLEYESSFSNEEAQKAQALRLASHLN
          AK.SWE.NSE.KLEQ.TIVKE.G.VYFKEGKYKQALLQ.KKIVSWLEYESSFS.EEAQK.QAL.L.S.LN
Retrocopy AKDSWEKNSEQKLEQNTIVKEQGSVYFKEGKYKQALLQCKKIVSWLEYESSFSSEEAQKSQALQLPSPLN

Parental  LAMCHLKLQAFSAAIESCNKALELDSNNEKGLFRRGEAHLAVNDFELARADFQKVLQLYPNNKAAKTQLA
          L.MC.LKLQAFSAAIESCNKALELDSNNEKGLF..GEAHLAVNDFELARADFQKVL.L.PNNKAA..QLA
Retrocopy LVMCQLKLQAFSAAIESCNKALELDSNNEKGLFCWGEAHLAVNDFELARADFQKVLHLCPNNKAAGAQLA

Parental  VCQQRIRRQLAREKKLYANMFERLAEEENKAKAEASSGDH
          VCQQ.IRRQLA..K..YANMFERLAEEENKAKAEA.SGDH
Retrocopy VCQQQIRRQLAQKK*HYANMFERLAEEENKAKAEACSGDH

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_2291 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007605	1 retrocopy	retro_btau_561,
Callithrix jacchus	ENSCJAG00000018746	1 retrocopy	retro_cjac_436,
Dasypus novemcinctus	ENSDNOG00000011244	1 retrocopy	retro_dnov_894,
Homo sapiens	ENSG00000004478	5 retrocopies	retro_hsap_3085, retro_hsap_4162, retro_hsap_4165, retro_hsap_4264, retro_hsap_4266,
Gorilla gorilla	ENSGGOG00000010471	4 retrocopies	retro_ggor_2120, retro_ggor_2852, retro_ggor_2854, retro_ggor_2855,
Macaca mulatta	ENSMMUG00000007405	1 retrocopy	retro_mmul_1969,
Nomascus leucogenys	ENSNLEG00000000800	1 retrocopy	retro_nleu_1406,
Nomascus leucogenys	ENSNLEG00000002835	1 retrocopy	retro_nleu_2291 ,
Nomascus leucogenys	ENSNLEG00000009356	5 retrocopies	retro_nleu_2009, retro_nleu_2628, retro_nleu_2728, retro_nleu_2730, retro_nleu_604,
Pongo abelii	ENSPPYG00000004149	4 retrocopies	retro_pabe_2607, retro_pabe_2611, retro_pabe_3383, retro_pabe_3518,
Pan troglodytes	ENSPTRG00000004529	3 retrocopies	retro_ptro_2083, retro_ptro_3000, retro_ptro_3001,