RetrogeneDB ID: retro_nleu_1752

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397307.1:10573335..10574520(+)
• Located in intron of: None

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_1752
GTGGTCACGGGACCTCAGGACCTTCCTGCGTGCTGCTGGCACTCATCTCCCCACCTTGGCGACTACTCCGTAGTCATGTC
CCCCGAGGACAAGGACAAGAAGCTGGAGGAAGGCAGCCCCGGGTACAGCCCCACTGAAGAGGTGCCAGTGAAGTCTGTGG
GGTAGAGGGTCCTGGACGGGCTGAAGCACTATTACCACGGCTTCTGCCTTCTCTGGATCGACACCAAGATAGCCACACAC
ATGCTCTGGAGGATTCTCAGTGGCCACGTGCTGACCCGGAAGCAAAGGGAGTTTGTCCATGTCTGTGCTGACTTCTTTTG
CCTGGTCCCTCTCCTCATCTTTGCGGTGGTGCTTTTCATGGAGTTGCTGTTGCCCATCATAGTGAAAATCTTTCCCAACA
TGTTGCTGTCCACATTTGAGACCCAGTCCATCAAGGAGGAGAGACCGAAGAAGCAGCTATGGGGGAGCTGGAACTGGCTA
AATTTCTCCAGGACACCATCGAGGAGATGGCCGTGAAGAACAAAGAAGCCAAGGGGAGGACTGCCAAAGACTTCTCCATG
TTTTTCCAGAAGATCCGAGAGACAGGAAAGACCTAACAACAAAGAAATCATGCGCTTTACCAAATTATTTGAGGATGAGC
TGACCCTGGATAACCTCACCTGCCAGCAGCTGGTGGCATTGTGTGAGCTGCTGGGTCTCCAGGCCATAGGCACCAACAAC
TTCCTGTGCTTCCAGCTCACCATGAGGTTGAGGTCCATAAAGGCCGACAATGAGTTGATTGCTGAGGAAGGGGTGGACAG
CCTGAATATCAAGGAATTGCTGTCGACATGTAGAACTCAAGGGATGTGGGCCCTTGGGGTCTCAGAAAACCACCTGAGGA
GCCTGCTGAAGCAGTGGCTGGACCTGCATTTGCATCAAGAGATCCCCATATCACTGCTCTTGTTGTCCTGAGCTATGTAT
CTCCCAGACACCCTCTCTCCTACTGACCAGCTCAAATCCACCTTGCAGACTCTTCCAGAGATAGTGGTGAAGGGAGCCCA
GGTGAAAGTGGACAAGGTGGAGGGTGAGCAGGTGGACAACAAAGTGAAAATGGAGGCCACAGTACAGGAGGAGATGGCCA
TCCAGCTGGAGCACAGGGAGAATGAGCTGCAGAAGCTATCTCAAAAAACGAAGTGGAAGAAGCCA

Alignment

ORF - retro_nleu_1752 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.3 %
• Parental protein coverage: 54.4 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VALGPRCLPVRGWHSSRPVGDDSVVEKSLKSLKDKNKKLEEGGPVYSPPAEVVVKKSLGQRVLDELKHYY
          V..GP..LP...WHSS...GD.SVV.....S..DK.KKLEEG.P.YSP..EV.VK.S.G.RVLD.LKHYY
Retrocopy VVTGPQDLPACCWHSSPHLGDYSVV----MSPEDKDKKLEEGSPGYSPTEEVPVK-SVG*RVLDGLKHYY

Parental  HGFRLLWIDTKIAARMLWRILNGHTLTRRERRQFLRICADLFRLVPFLVFVVVPFMEFLLPVAVKLFPNM
          HGF.LLWIDTKIA..MLWRIL.GH.LTR..R..F...CAD.F.LVP.L.F.VV.FME.LLP..VK.FPNM
Retrocopy HGFCLLWIDTKIATHMLWRILSGHVLTRKQR-EFVHVCADFFCLVPLLIFAVVLFMELLLPIIVKIFPNM

Parental  LPSTFETQSLKEERLKKEL-RVKLELAKFLQDTIEEMALKNKAAK-GSATKDFSVFFQKIRETGERPSNE
          L.STFETQS.KEER.KK.L....LELAKFLQDTIEEMA.KNK.AK.G...K..S..F....E..ERP.N.
Retrocopy LLSTFETQSIKEERPKKQL<MGELELAKFLQDTIEEMAVKNKEAK>GGLPKT-SPCFSRRSERQERPNNK

Parental  EIMRFSKLFEDELTLDNLTRPQLVALCKLLELQSIGTNNFLRFQLTMRLRSIKADDKLIAEEGVDSLNVK
          EIMRF.KLFEDELTLDNLT..QLVALC.LL.LQ.IGTNNFL.FQLTMRLRSIKAD..LIAEEGVDSLN.K
Retrocopy EIMRFTKLFEDELTLDNLTCQQLVALCELLGLQAIGTNNFLCFQLTMRLRSIKADNELIAEEGVDSLNIK

Parental  ELQAACRARGMRALGVTEDRLRGQLKQWLDLHLHQEIPTSLLILSRAMYLPDTLSPADQLKSTLQTLPDI
          EL...CR..GM.ALGV.E..LR..LKQWLDLHLHQEIP.SLL.LS.AMYLPDTLSP.DQLKSTLQTLP.I
Retrocopy ELLSTCRTQGMWALGVSENHLRSLLKQWLDLHLHQEIPISLLLLS*AMYLPDTLSPTDQLKSTLQTLPEI

Parental  VAKEAQVKAAEVEGEQVDNKAKLEATLQEEAAIQQEHREKELQKRSEAAKDVEP
          V.K.AQVK...VEGEQVDNK.K.EAT.QEE.AIQ.EHRE.ELQK.S...K...P
Retrocopy VVKGAQVKVDKVEGEQVDNKVKMEATVQEEMAIQLEHRENELQKLSQKTKWKKP

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_1752 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,