RetrogeneDB ID: retro_nleu_2731

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397411.1:2784454..2785627(+)
• Located in intron of: ENSNLEG00000011057

Retrocopy information

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

Parental gene information

• Parental gene symbol: LETM1
• Ensembl ID: ENSNLEG00000000067
• Aliases: None
• Description: leucine zipper-EF-hand containing transmembrane protein 1 [Source:HGNC Symbol;Acc:6556]

Sequence

>retro_nleu_2731
AGCTTTCTGCGTTTCCAGCTCACCATGCGGCTGTGCTCCATAAGGCAGAGGACAAGCTGTTTGCTGAGGAAGGGGTGGAC
AGCCTGAACGTCAAGGAGCTGCAGGTGGCATGTCGGGCACGAGGCATGCGGACCCTGGGCGTCACGGAAAACCGCCTGAG
GGGCCAGCTGAAGCAGTGGCTGGACCTGCACCTGCATCAGGAGATCCCCACATCGCTGCTCATCCTGTTCCGGACCGTGT
ACCTCCTGGCCACCCTCTCACCAGCTGACCAGCTCAAGTCCACACTGCAGACCCTCCCAGAGATTGTGGCAAAGGAAGCG
CAGGTGAAAGTGGCCGAGGTGGAGGGCAAGCACGTGGACAAGGCCAAGCTGGAGGCCACACTGCAGGAGGAGGCGACCAT
CCAGCAGGAGCACCGCAAGAAGGCGCTGCAGAAGCGTCCGGAGGTGGCGAAGGATGTTGAGCCCGACTGTGTGAAGCCGC
TCCCCAAAGGCCAGGGGCCCAGCTGCAGCGAGAAGTGCCTGACACAGTCCTGCAGTCAGAGACCCTGAAGGACACTGCCC
CCGTGCTGGACGGCTTGAAGGAGGAAGAGATCACTAAGGAGGAAATCAACATCCTCAGCAACGCCTGCTCTAAGCTGCAG
GAACAGAAGTCACTCACCAGGGAGAAGGAGGCGCTGGAGCTGCTGAAGGAGGACATGCAGGACTACAGTGAGGACTTGCA
GGAGATCAAGAAGGAACTTTCAAAGACTGGTGAAGAAAAATACGTGGAAGAATCTAAAGCCGGCAAGAGATTGACAAAAA
GGGTGCAGCAGATGATCGGGCAGATTGATGGCTTGATCTCGCAGCTGGAGATGGACCAGTGGGCCAGCAAGCTGGCCCTG
GCCAAGGGCGTACCCATGGGGGAGAACGTCATCAGTGTCGCCCAGCTCATCAACGCCATGAAGCAAGTCAAGCACATTCC
CGAAAGCAAGCTCACCAGCCTGGCTGCAGCACTGGATGAAAATAAGGATGGCAAGGTCAACTTCGACAACGTCGTCAAGG
TGATTGAGCTGGTGGACAAAGAAAATGTTCACATTTCCACCAGTCAGGTGGCCAAGATTGTAGCAACACTGGAAAAACAG
GAGAAGGGGAGGAGAAGGAGAAGGTGGAGAAGAAGGTCGCAGAGGTGAAGAGC

Alignment

ORF - retro_nleu_2731 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.29 %
• Parental protein coverage: 53.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  NFLRFQLTMRLRSI-KADDKLIAEEGVDSLNVKELQAACRARGMRALGVTEDRLRGQLKQWLDLHLHQEI
          .FLRFQLTMRL.SI.KA.DKL.AEEGVDSLNVKELQ.ACRARGMR.LGVTE.RLRGQLKQWLDLHLHQEI
Retrocopy SFLRFQLTMRLCSI<KAEDKLFAEEGVDSLNVKELQVACRARGMRTLGVTENRLRGQLKQWLDLHLHQEI

Parental  PTSLLILSRAMYLPDTLSPADQLKSTLQTLPDIVAKEAQVKAAEVEGEQVDNKAKLEATLQEEAAIQQEH
          PTSLLIL.R..YL..TLSPADQLKSTLQTLP.IVAKEAQVK.AEVEG..VD.KAKLEATLQEEA.IQQEH
Retrocopy PTSLLILFRTVYLLATLSPADQLKSTLQTLPEIVAKEAQVKVAEVEGKHVD-KAKLEATLQEEATIQQEH

Parental  REKELQKRSEAAKDVEPERVV-AAPQRPGTEPQPEMPDTVLQSETLKDTAPVLEGLKEEEITKEEIDILS
          R.K.LQKR.E.AKDVEP..V..AAPQRPG...Q.E.PDTVLQSETLKDTAPVL.GLKEEEITKEEI.ILS
Retrocopy RKKALQKRPEVAKDVEPDCVK<AAPQRPGAQLQREVPDTVLQSETLKDTAPVLDGLKEEEITKEEINILS

Parental  DACSKLQEQKKSLTKEKEELELLKEDVQDYSEDLQEIKKELSKTGEEKYVEESKASKRLTKRVQQMIGQI
          .ACSKLQEQK.SLT.EKE.LELLKED.QDYSEDLQEIKKELSKTGEEKYVEESKA.KRLTKRVQQMIGQI
Retrocopy NACSKLQEQK-SLTREKEALELLKEDMQDYSEDLQEIKKELSKTGEEKYVEESKAGKRLTKRVQQMIGQI

Parental  DGLISQLEMDQQAGKLAPANSMPTGENVISVTELINAMKQVKHIPESKLTSLAAALDENKDGKVNIDDLV
          DGLISQLEMDQ.A.KLA.A...P.GENVISV..LINAMKQVKHIPESKLTSLAAALDENKDGKVN.D..V
Retrocopy DGLISQLEMDQWASKLALAKGVPMGENVISVAQLINAMKQVKHIPESKLTSLAAALDENKDGKVNFDNVV

Parental  KVIELVDKEDVHISTSQVAEIVATLEKEEK-VEEKEKAKEKAEKEVAEVKS
          KVIELVDKE.VHISTSQVA.IVATLEK.EK..EEKEK.....EK.VAEVKS
Retrocopy KVIELVDKENVHISTSQVAKIVATLEKQEK<GEEKEK----VEKKVAEVKS

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_2731 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001859	1 retrocopy	retro_cjac_1529,
Homo sapiens	ENSG00000168924	1 retrocopy	retro_hsap_2019,
Gorilla gorilla	ENSGGOG00000002923	2 retrocopies	retro_ggor_1158, retro_ggor_1159,
Nomascus leucogenys	ENSNLEG00000000067	2 retrocopies	retro_nleu_1752, retro_nleu_2731 ,
Otolemur garnettii	ENSOGAG00000014883	1 retrocopy	retro_ogar_20,
Pongo abelii	ENSPPYG00000014533	1 retrocopy	retro_pabe_1655,
Ictidomys tridecemlineatus	ENSSTOG00000014167	1 retrocopy	retro_itri_160,