RetrogeneDB ID: retro_nleu_954

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397277.1:27341756..27342795(+)
• Located in intron of: ENSNLEG00000012296

Retrocopy information

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

Parental gene information

• Parental gene symbol: KDELC1
• Ensembl ID: ENSNLEG00000007858
• Aliases: None
• Description: None

Sequence

>retro_nleu_954
CCGGAAACCATTGCTCAGATTCAGAGAGACCTGGCACAGTTCCCTACTGTGGATCCAGAAAAGATTGCAGTAGAAATCCC
AAAAAGATTTGGACAGGGGCAGAGCCTGTGTCACTAAACTTTAAAAGATAACAAAGTTTATATGAAGACTCATGGTGAAC
ATGTAGGTTTTAGAATTTTCATGGATGCCATACTACTTTCTTTGACTAGAAAGGTGAAGATGCCAGATGTAGAGTTCTTT
GTTAATTTGGCAGACTGGCCTTTGCTTTGGAAAAAAAGAAATCCAATTCAAACATCCATCCGACCTTTTCCTGGTGTGGC
TGCACAGATTCCAAGGATATCGTGATGCCCACCTATGACTTGACTGTTTTAGAAACCATGGGCTGGGTAAGTCTGGATAT
GATGTCTGTGCAAGCTAACACGGGTCCTCCCTGGGAAAGCAAAAACTCCACAGCTGTCTGGAGAGGGCGAGACAGCCGCA
AAGGAGACTTGAGCTGGTTAAACTCAGTAGAATCACCTTGAGTTCATAGACGCTGCTTTCACCAACTTTTTCTTCTTTAA
ACATGATGAAAACCTGTATGGTCCCATTGTGAAACACATTTCATTTTTTTATTTCTTCAAGCATAAGTATCAAATAAATA
TCGATGGCATCATAGCAGCTTATCACCTGCCATATTTACTAGTTAGTGACAGTCTTGTGCTGAAGCCAAGACTCTGTCGA
CTATGAACATTTTAACAATGAGCTGCAGCCCTGGAAACACTACATTCCAGTTAAAAGCAACCTGAGTGATCTTCTAGAAA
AACTTAAATGGGCAAAAGATCACAATGAAGTGGCCAAAAAGATAGCAAAAGCAGGACAAGAATTTGCAAGAAATAATCTC
ATGGATGGTTACATATTCTGTTATTATTTCAAACTTTTCCAGGAATATGCCAATTTACAAGTGAATGGGCCCCAAATCTG
AGAGGGCATGAAAAGGGTAGAATCACAGACTGAGAATGACCTCTTCCTTTGCCATAGGAAAAAGACCAAAGATGAACTC

Alignment

ORF - retro_nleu_954 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.07 %
• Parental protein coverage: 69.46 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PETIAQIQRDLAHFPAVDPEKIAVEIPKRFGQRQSLCHYTLKDNKVYIKTHGEHVGFRIFMDAILLSLTR
          PETIAQIQRDLA.FP.VDPEKIAVEIPKRFGQ.QSLCH.TLKDNKVY.KTHGEHVGFRIFMDAILLSLTR
Retrocopy PETIAQIQRDLAQFPTVDPEKIAVEIPKRFGQGQSLCH*TLKDNKVYMKTHGEHVGFRIFMDAILLSLTR

Parental  KVKMPDVEFFVNLGDWPLEKKKSN-SN--IHPIFSWCGSTDSRDIVMPTYDLTDSVLETMGRVSLDMMSV
          KVKMPDVEFFVNL.DWPL..KK.N.SN..IHP.FSWCG.TDS.DIVMPTYDLT..VLETMG.VSLDMMSV
Retrocopy KVKMPDVEFFVNLADWPLLWKKRN<SNSNIHPTFSWCGCTDSKDIVMPTYDLT--VLETMGWVSLDMMSV

Parental  QANTGPPWESKNSTAVWRGRDSRK-ERLELVKLSR-KHPELIDAAFTNFFFFKHDESLYGPIVKHISFFD
          QANTGPPWESKNSTAVWRGRDSRK..RLELVKLSR..H.E.IDAAFTNFFFFKHDE.LYGPIVKHISFF.
Retrocopy QANTGPPWESKNSTAVWRGRDSRK<RRLELVKLSR<NHLEFIDAAFTNFFFFKHDENLYGPIVKHISFFY

Parental  FFKHKYQINIDGTVAAYRLPYLLVGDSVVLK-QDSIYYEHF-TMAAAWKHYIPVKSNLSDLLEKLKWAKD
          FFKHKYQINIDG..AAY.LPYLLV.DS.VLK.QDS..YEHF......WKHYIPVKSNLSDLLEKLKWAKD
Retrocopy FFKHKYQINIDGIIAAYHLPYLLVSDSLVLK>QDSVDYEHFNNELQPWKHYIPVKSNLSDLLEKLKWAKD

Parental  HDEEAKKIAKAGQEFARNNLMGDDIFCYYFKLFQEYANLQVSEPQIREGMKRVEAQTEDDLFPCTCHRKK
          H.E.AKKIAKAGQEFARNNLM...IFCYYFKLFQEYANLQV..PQI.EGMKRVE.QTE.DLF...CHRKK
Retrocopy HNEVAKKIAKAGQEFARNNLMDGYIFCYYFKLFQEYANLQVNGPQI*EGMKRVESQTENDLF--LCHRKK

Parental  TKDEL
          TKDEL
Retrocopy TKDEL

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_954 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000007858	1 retrocopy	retro_nleu_954 ,
Pongo abelii	ENSPPYG00000005483	1 retrocopy	retro_pabe_2683,
Rattus norvegicus	ENSRNOG00000011740	1 retrocopy	retro_rnor_823,