RetrogeneDB ID: retro_nleu_2729

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397411.1:1883725..1885037(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTCD3
• Ensembl ID: ENSNLEG00000002493
• Aliases: None
• Description: None

Sequence

>retro_nleu_2729
ATGGCGGCTGTAGCTGCTGTTCACTGGCTGGGGCTCTGCAGCAGGCTTGACCAGCCACTGACGGGTCAGCCGGCAGGTCT
GTGTGAACAGGCACACAGCTGCAGATTTTATTCTGGAAGTGCAACCCTCTCAAATATTGAAGGAACTGATACAACAGGGA
TTGAAGAAGTAGTAATTCCAAAAAAGAAAACTTGGGATAAAGTAGCCATTCTTCAGGCTCTTGCATCCACAGTAAACAGA
GTTCCCATGGCTGTATCTTGTGCGTTTCAAGATAATCCTTACCTGATACCAACATCCTCTTCAGAATCTCGTTCATTTTT
ACTGGCAAAGAAATCTGGGGAGAATACGGCCAAGTTCATTATTAATTCATACTCCAAATATTTTCAGAAGAACATAGCCG
AACCTCATATACTGTGTTTAATGCCTGAGTACTTTGAACCTCAGATCAAGGACATAAGTGAAGCCACCCTCAAGGAACGA
ATCAAGCTCAGAAAAGTCAAAGCCTCTGTGGACATGTGTGATCAGCTTTTGCAAGCAGGAACCACGGTGTCTCCTGGAAC
AATACATAGTCTTTTGGATTTATTGTGTTACTGTGGTGACCAGGAGCTCTCAGCTGATGATCATTTTCAACAAACTGAAC
AGCCAGAAGAATTGGAAGAGGAAAATAATGAGAGGTCTAGGAGGAAAGCTGGTCATCAGTTTGGAGTTACCTGGTGAGCA
AAAAACAGCGCTGAGAGAATGTTTTCTGTAATGCCAGAGAAAAATGCACATTCCTATTGCACAATGATCCGAGGAATGTT
GAAGCACCAAGCTTATGAGCAGGCATTAAACCTGTACAGTGAGTTACTAAACAACAGACTCTGTGCTGATGTATACACAT
TTAATGCAGTGATTGAAGCAACAGTATTGGTGATCAATGAGAAATTTGAGGAAAAGTGGAATAATATACTGGAGCTGCTA
AGACAAATGGTTGCACAGAAGATGAAACCAAATCTACAGACTTTTAATGCCATTCTGAAATGTCTCCGAAGATTTTATGT
ACTTGCAAGATTGCCAGCCTTACAGATTCTACGTGAAATGAAAGCCATCAGAATAGAACCCTCGCTTGCAACATATCACC
ATATTATTCAGCTGTTTTATCAGCCTGGAAGCCCTTCAAAGGGATCATCTTTCATCATCTATGATATAATGAGCGAATTA
ATGGGAAAGAGATTTTCCTCCAAAGGACCTGGATGATGATAAGTTTTTTCAGTCAGCCATGAGAGTATCCTCATCTCTCA
GAAATCTAGAACTTGCCTACCAAATACATGGG

Alignment

ORF - retro_nleu_2729 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 63.43 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAAVAAVRWLRLRSRLGQPLTGRRARLCEQARSCRFYSGSATLSKVEGTDITGIEEVVIPKKKTWDKVAV
          MAAVAAV.WL.L.SRL.QPLTG..A.LCEQA.SCRFYSGSATLS..EGTD.TGIEEVVIPKKKTWDKVA.
Retrocopy MAAVAAVHWLGLCSRLDQPLTGQPAGLCEQAHSCRFYSGSATLSNIEGTDTTGIEEVVIPKKKTWDKVAI

Parental  LQALASTVNRDTTAVPYVFQDDPYLIPASSLESRSFSLAKKSGENVAKFIINSYPKYFQKDIAEPHIPCL
          LQALASTVNR...AV...FQD.PYLIP.SS.ESRSF.LAKKSGEN.AKFIINSY.KYFQK.IAEPHI.CL
Retrocopy LQALASTVNRVPMAVSCAFQDNPYLIPTSSSESRSFLLAKKSGENTAKFIINSYSKYFQKNIAEPHILCL

Parental  MPEYFEPQIKDVSEAALKERIELRKVKASVDMFDQLLQAGTTVSLETTNSLLDLLCYYGDQEPSTDYHFQ
          MPEYFEPQIKD.SEA.LKERI.LRKVKASVDM.DQLLQAGTTVS..T..SLLDLLCY.GDQE.S.D.HFQ
Retrocopy MPEYFEPQIKDISEATLKERIKLRKVKASVDMCDQLLQAGTTVSPGTIHSLLDLLCYCGDQELSADDHFQ

Parental  QTEQSEALEEENDETSRRKAGRQFGVTWQAKNNAERIFSLMPEKNAHSYCTMIRGMVKHRACEQALNLYT
          QTEQ.E.LEEEN.E.SRRKAG.QFGVTW.AKN.AER.FS.MPEKNAHSYCTMIRGM.KH.A.EQALNLY.
Retrocopy QTEQPEELEEENNERSRRKAGHQFGVTW*AKNSAERMFSVMPEKNAHSYCTMIRGMLKHQAYEQALNLYS

Parental  ELLNNRLRADVYTFNAMIEATVFVINEKFEEKWSKILELLRHMVAQKVKPNLQTFNTILKCLRRFHVLAR
          ELLNNRL.ADVYTFNA.IEATV.VINEKFEEKW..ILELLR.MVAQK.KPNLQTFN.ILKCLRRF.VLAR
Retrocopy ELLNNRLCADVYTFNAVIEATVLVINEKFEEKWNNILELLRQMVAQKMKPNLQTFNAILKCLRRFYVLAR

Parental  SPALQILREMKAIGIEPSLATYHHIIQLFDQRGNPSKKSSFIIYDIMNELMGKRFS-PKDPDDDKFFQSA
          .PALQILREMKAI.IEPSLATYHHIIQLF.Q.G.PSK.SSFIIYDIM.ELMGKRFS.PKD.DDDKFFQSA
Retrocopy LPALQILREMKAIRIEPSLATYHHIIQLFYQPGSPSKGSSFIIYDIMSELMGKRFS>PKDLDDDKFFQSA

Parental  MSICSSLRDLELAYQIHG
          M...SSLR.LELAYQIHG
Retrocopy MRVSSSLRNLELAYQIHG

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_2729 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000132300	1 retrocopy	retro_hsap_2017,
Gorilla gorilla	ENSGGOG00000001793	1 retrocopy	retro_ggor_1461,
Nomascus leucogenys	ENSNLEG00000002493	1 retrocopy	retro_nleu_2729 ,
Pongo abelii	ENSPPYG00000012216	1 retrocopy	retro_pabe_1653,