RetrogeneDB ID: retro_nleu_2553

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397371.1:4112944..4113648(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SKP2
• Ensembl ID: ENSNLEG00000016025
• Aliases: None
• Description: None

Sequence

>retro_nleu_2553
GTGCACAAGAACCACCTTTAAGAGATTCCAGACCAGAGTAGCAATGTTACCACCAGCTTCGTGTGGGGATAGGATTCCAG
CAAGACTTCTGAACTACTGTCAGGCATCGGGGTCTACGCCCTGGAGAAGGAGGAGGCAGACAGTAAGAATATCCCCAAGG
AACTGCTCTAAAACCTGGGCCAATCACACAGCCACCCAAGGAAATGGCTGAAGAGCAAAAGGAATGACAAAGACTGTGAT
CATCAACAGGCCTAAACTAAATGGAGAGAACTTTCCAGGTGTTTCATGGGACTCCCTTCCAGATGAGCTGCTCTTGGGAA
TATTTTCCTGTCTGCGCCTCACTGAGCTGCTAAAGGCCTCTGATGTTTTAAGAGATGGTATTGCCCTAGCATTTGTTGAG
TCTCTGTGGCAGACTTTATACCTCACAGGTAAAAATCTGAAGCCAGATGTGATTAGTGTGGGCTGGTTGCCTTTCACTGC
CAACAATCATTTATGACCAACCATTGGTTGAACATTTCAGCCCTCTGCATATACAGCAGAGGGATGTGTTGAACTCAGTT
ATAGATGTGTCTGCCCTCCATGGCATTCTGTCTTGGGGCTCCAAGCTGCAGAATCTAAGCTTTCTGGAAGACCTATGGCT
CTCAGATCCCATTATCAATAATCTTGCACAGAAGTCAAATTTAGTGCAACTGGGTGTTCTGGGT

Alignment

ORF - retro_nleu_2553 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.8 %
• Parental protein coverage: 56.37 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MHRKHLQEIPDLSSNVATSFTWGWDSSKTSELLSGMGVSALEKEEPDSENIPQELLSNLGHPESPPRKRL
          .H..HL.EIPD.SSNV.TSF.WG.DSSKTSELLSG.GV.ALEKEE.DS.NIP.ELL.NLG...S.PRK.L
Retrocopy VHKNHL*EIPDQSSNVTTSFVWG*DSSKTSELLSGIGVYALEKEEADSKNIPKELL*NLGQSHSHPRKWL

Parental  KSKGSDKD-FVIVRRPKLNRENFPGVSWDSLPDELLLGIFSCLCLPELLKVSGVC-KRWY-RLASDESLW
          KSK..DKD...I.R.PKLN.ENFPGVSWDSLPDELLLGIFSCL.L.ELLK.S.V..KRWY..LA..ESLW
Retrocopy KSKRNDKD>VIINR-PKLNGENFPGVSWDSLPDELLLGIFSCLRLTELLKASDVL<KRWY>ALAFVESLW

Parental  QTLDLTGKNLHPDVTGRLLSQGVIAF-RCPRSFM-DQPLAEHFSPFRVQHMDLSNSVIEVSTLHGILSQC
          QTL.LTGKNL.PDV.....S.G...F..C..SFM.DQPL.EHFSP...Q..D..NSVI.VS.LHGILS..
Retrocopy QTLYLTGKNLKPDV----ISVGWLPF<HCQQSFM<DQPLVEHFSPLHIQQRDVLNSVIDVSALHGILSWG

Parental  SKLQNLS-LEGLRLSDPIVNNLAQNSNLVRLNLSG
          SKLQNLS.LE.L.LSDPI.NNLAQ.SNLV.L...G
Retrocopy SKLQNLSFLEDLWLSDPIINNLAQKSNLVQLGVLG

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_2553 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013562	4 retrocopies	retro_btau_1108, retro_btau_1612, retro_btau_525, retro_btau_555,
Callithrix jacchus	ENSCJAG00000018275	1 retrocopy	retro_cjac_2367,
Cavia porcellus	ENSCPOG00000013303	1 retrocopy	retro_cpor_1166,
Nomascus leucogenys	ENSNLEG00000016025	1 retrocopy	retro_nleu_2553 ,
Oryctolagus cuniculus	ENSOCUG00000009154	1 retrocopy	retro_ocun_158,
Pelodiscus sinensis	ENSPSIG00000008375	1 retrocopy	retro_psin_28,
Rattus norvegicus	ENSRNOG00000016823	1 retrocopy	retro_rnor_621,