RetrogeneDB ID: retro_nleu_1121

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397282.1:19502837..19504000(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSNLEG00000012555
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MAP2K2
• Ensembl ID: ENSNLEG00000003013
• Aliases: None
• Description: None

Sequence

>retro_nleu_1121
ACCATCAACCCTACCATCGCCGAGGGCCCGTCCCCAGCCAGCGAGGGCGCCTGTGAGGCAAACCTGGTGGACCTGCAGAA
GAAGCTGGAGGAGCTGGAACTTGACAAGCAGCAGAAGGGGCCTGAAGCCTTTCTCACCCAGAAAGCCAAGGTCGGCGAAC
TCAAAGACGATGACTTCGAAAGGATCTCAGAGCTGGGCGCGGGCAATGGCGGGGTGGTCACCAAAGTCCAGCACAGACCC
TCGGGCCTCATCACGGCCAGGAAGTTGATCTGCCTTGAGATCAAGCCGGCCATCCGGAACCAGATCATCCGCGAGCAACA
GGTCCTGCACGAGGGCAACTCGCCGTACATCGTGGGCTTCTACGGGGCCTTCTGCAGTGACGGGGAGATCAGCATCTGCA
TGGAGCACATGGATGGCGGCTCCCTGGACCAGGTGCTGAAAGAGGCCAAGAGGATTCCCGAGCAGATCCTGGGGAAAGTC
AGCATTGCGGTTCTCCGGGGCTTGGCGTACCTCCGAGAGAAGCACCAGATCATGCACCGAGATGTGAAGCCCTCCAACAT
CCTCGTGAACTCTAGAGGGTAGATCAAGCTGTGTGACTTCGGGGTGAGCGGCCAGCTCATCGACTCCATGGCCAACTCCT
TCGTGGGCACGCGCTCCTACATGGCTCCGGAGCGGTTGCAGGGCACACATTACTTGGTGCAGTCGGACATCGGGAGCATG
GGCCTGTCCCTGGTGGAGCTGGCCATCAGAAGGTACCCCATCCCCCCGCCCGACGCCAAGGAGCTGGAGGCCATCTTTGG
CCCGCCAGTGGTCGACAGGGAAGAAGTAGAGCCTCACAGCATCTCGCCTCGGCCAAGGCCCCCAGGGCGCCCCATCAGCG
GTCACGGGGTGGACAGCCGGCCCGCCATGGCCATCTTTGAACTGCTGGACTATATTGTGAACGAGCCGCCTCCTAAGCTG
CCCAACGGTGTGTTCACCCCCGACTTCCAGGAGTTTGTCAATAAATGCCTCATCAAGAACCCAGCGGAGCGGGCAGACCT
GAAGATGCTCACAAAACCACGCCTTTCATCAAGCGGTCCGAGGTGGAGGAAGTGGATTTTGCCTGCTGATTGTGTAAAAC
CCTGCAGCTGAACCAGCCCGGCACACCCACGCGCACCGCCATG

Alignment

ORF - retro_nleu_1121 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.74 %
• Parental protein coverage: 63.49 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TINPTIAEGPSPTSEGASEANLVDLQKKLEELELDEQQKKRLEAFLTQKAKVGELKDDDFERISELGAGN
          TINPTIAEGPSP.SEGA.EANLVDLQKKLEELELD.QQK...EAFLTQKAKVGELKDDDFERISELGAGN
Retrocopy TINPTIAEGPSPASEGACEANLVDLQKKLEELELDKQQKGP-EAFLTQKAKVGELKDDDFERISELGAGN

Parental  GGVVTKVQHRPSGLIMARKLIHLEIKPAIRNQIIRELQVLHECNSPYIVGFYGAFYSDGEISICMEHMDG
          GGVVTKVQHRPSGLI.ARKLI.LEIKPAIRNQIIRE.QVLHE.NSPYIVGFYGAF.SDGEISICMEHMDG
Retrocopy GGVVTKVQHRPSGLITARKLICLEIKPAIRNQIIREQQVLHEGNSPYIVGFYGAFCSDGEISICMEHMDG

Parental  GSLDQVLKEAKRIPEEILGKVSIAVLRGLAYLREKHQIMHRDVKPSNILVNSRGEIKLCDFGVSGQLIDS
          GSLDQVLKEAKRIPE.ILGKVSIAVLRGLAYLREKHQIMHRDVKPSNILVNSRG.IKLCDFGVSGQLIDS
Retrocopy GSLDQVLKEAKRIPEQILGKVSIAVLRGLAYLREKHQIMHRDVKPSNILVNSRG*IKLCDFGVSGQLIDS

Parental  MANSFVGTRSYMAPERLQGTHYSVQSDIWSMGLSLVELAIGRYPIPPPDAKELETIFRPVVRRGKKGEPH
          MANSFVGTRSYMAPERLQGTHY.VQSDI.SMGLSLVELAI.RYPIPPPDAKELE.IF.P.V......EPH
Retrocopy MANSFVGTRSYMAPERLQGTHYLVQSDIGSMGLSLVELAIRRYPIPPPDAKELEAIFGPPVVDREEVEPH

Parental  K-HVGSRPPGRPISGHGVDSRPAMAIFELLDHIVNEPPPKLPNGVFTPDFQEFVNKCLIKNPAERADLKM
          ......RPPGRPISGHGVDSRPAMAIFELLD.IVNEPPPKLPNGVFTPDFQEFVNKCLIKNPAERADLKM
Retrocopy SISPRPRPPGRPISGHGVDSRPAMAIFELLDYIVNEPPPKLPNGVFTPDFQEFVNKCLIKNPAERADLKM

Parental  LT-NHT-FIKRSEVEEVDFAGWLC-TLRLNQPGTPTRTAV
          LT.NH..FIKRSEVEEVDFA..LC.TL.LNQPGTPTRTA.
Retrocopy LT>NHA>FIKRSEVEEVDFAC*LCKTLQLNQPGTPTRTAM

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_1121 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000015084	1 retrocopy	retro_cjac_4061,
Equus caballus	ENSECAG00000009157	2 retrocopies	retro_ecab_668, retro_ecab_968,
Homo sapiens	ENSG00000126934	1 retrocopy	retro_hsap_3785,
Gorilla gorilla	ENSGGOG00000008832	1 retrocopy	retro_ggor_115,
Nomascus leucogenys	ENSNLEG00000003013	1 retrocopy	retro_nleu_1121 ,
Otolemur garnettii	ENSOGAG00000001658	1 retrocopy	retro_ogar_576,
Pan troglodytes	ENSPTRG00000010294	1 retrocopy	retro_ptro_2566,