RetrogeneDB ID: retro_nleu_1485

Retrocopy location

• Organism: Gibbon (Nomascus leucogenys)
• Coordinates: GL397296.1:4949899..4950956(+)
• Located in intron of: ENSNLEG00000018025

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRMT2B
• Ensembl ID: ENSNLEG00000007522
• Aliases: None
• Description: None

Sequence

>retro_nleu_1485
GCTCAAGGTGAAATTTTACAAAGACTAGAGTCTCACATCCAAATGCTCGATGAAGTCAATGTGACAACAGCTGCACCCAA
ATCTGAGGGGCTGTCTTGTCTTCTCCATCCTATTATACCATCTCCTGTTGTCAGTGGCTGCAGAAATAAGTCCACCTTCT
CTGTGAATCAGTGTCCAGATGGCAATCCAAAGACTGTGGAATATGACCTGGGAACTTGAAGAGATGGGAATATCGTCTGT
GTACAGTCTAACCATCTGAAAAACATCCCTGAGAAACACAATCAGGTGGCACAGTACTATGAAGTATTCCTTCCACAGTC
TCCAACAGAGCCCTGCCTTCTGCTTCGTGAAGGTCGATACTGGTGTGAGCTCACAGTCCGCACCAATAGCCTAAGGCACA
CAATGGCTGTCATCACATTCCATCCCCAGGAATTAAGTCCAGAGGAGCTCCATGTTCAGAAGGAGACTGTAAAGGAATTT
TTCATTAAAGGTCCTGGAGCAGTCTGTGACTTGACTTCACTTGACTTCCAGGAAAGCAGGACCCGTTTCAGCCATCATCA
GTCCGCCTACCAGCTCTTATTTGGAGAACCTCATATCTTTAAAGATCTCCTGGGCTTGAAGGTCTGCATCTCTCCAGATG
CCTTTTTCCAGATTAACACTGCTGGTGCAGAGATGCTATATTGGATTGTGGGGAAGCTGAGTGGAGTGAACTCTAACACC
ATCCTCCTCGACATCTGCTGTGGAACCGGTGTGATCAGCCTCCCTCTGGCTCAGCTACATCGCAGGTCCTTGGGATTTTG
TTGGTGGGGCAGGCAGTGGAGGATGCCAGGCAGACTGCAGCCTACAGTGGCATCACCAGCTTTGAGTTTCATACTGGTCA
AGCAGAGATTTTTCCAGGGCTGCTAAAGTCAAAGGAAGATGTACAGTTAATTGTTGCTATGTGAACCCAGCCCATGCTGA
ACTGCATTACAAGGAAGTTCAAGCCATTTGAAACTTCAAGGCCCTCCGCATACTAGCTTTTGTTTCCTGCAAGCCCCATG
ATGAAACCACAAGGAAT

Alignment

ORF - retro_nleu_1485 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.03 %
• Parental protein coverage: 70.44 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AQKKILQRLESYIQMLNGVSVTTAVPISERLPCLLHPIIPSPVINGYRNKSTFSVNRGPDGNPKTVGFYL
          AQ..ILQRLES.IQML..V.VTTA.P.SE.L.CLLHPIIPSPV..G.RNKSTFSVN..PDGNPKTV...L
Retrocopy AQGEILQRLESHIQMLDEVNVTTAAPKSEGLSCLLHPIIPSPVVSGCRNKSTFSVNQCPDGNPKTVEYDL

Parental  GTWRDGNIVCVQSNHLKNIPEKHSQVAQYYEVFLRQSPLEPCLVFHEGGYWRELTVRTNSQGHTMAIIIF
          GT.RDGNIVCVQSNHLKNIPEKH.QVAQYYEVFL.QSP.EPCL...EG.YW.ELTVRTNS..HTMA.I.F
Retrocopy GT*RDGNIVCVQSNHLKNIPEKHNQVAQYYEVFLPQSPTEPCLLLREGRYWCELTVRTNSLRHTMAVITF

Parental  HPQKLSQEELHVQKETVKEFFIRGPGAACDLTSLYFQESTMTRCSHQQSPYQLLFGEPYIFEELLSLKIR
          HPQ.LS.EELHVQKETVKEFFI.GPGA.CDLTSL.FQES..TR.SH.QS.YQLLFGEP.IF..LL.LK..
Retrocopy HPQELSPEELHVQKETVKEFFIKGPGAVCDLTSLDFQES-RTRFSHHQSAYQLLFGEPHIFKDLLGLKVC

Parental  ISPDAFFQINTAGAEMLYRTVGELTGVNSDTILLDICCGTGVIGLSLAQ-HTSRVLGIELVEQAVEDARW
          ISPDAFFQINTAGAEMLY..VG.L.GVNS.TILLDICCGTGVI.L.LAQ..TS.VLGI.LV.QAVEDAR.
Retrocopy ISPDAFFQINTAGAEMLYWIVGKLSGVNSNTILLDICCGTGVISLPLAQ<ATSQVLGILLVGQAVEDARQ

Parental  TAAFNGITNSEFHTGQAEKILPGLLKSKEDGQSIVAV-VNPARAGLHYKVIQAIRNFRAIRTLVFVSCKL
          TAA..GIT..EFHTGQAE.I.PGLLKSKED.Q.IVA..VNPA.A.LHYK..QAI.NF.A.R.L.FVSCK.
Retrocopy TAAYSGITSFEFHTGQAE-IFPGLLKSKEDVQLIVAM<VNPAHAELHYKEVQAI*NFKALRILAFVSCKP

Parental  HGESTRN
          H.E.TRN
Retrocopy HDETTRN

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_1485 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004570	1 retrocopy	retro_cjac_1676,
Homo sapiens	ENSG00000188917	1 retrocopy	retro_hsap_272,
Gorilla gorilla	ENSGGOG00000023759	1 retrocopy	retro_ggor_319,
Macropus eugenii	ENSMEUG00000006532	2 retrocopies	retro_meug_1325, retro_meug_74,
Macaca mulatta	ENSMMUG00000010394	1 retrocopy	retro_mmul_567,
Monodelphis domestica	ENSMODG00000025630	1 retrocopy	retro_mdom_77,
Nomascus leucogenys	ENSNLEG00000007522	1 retrocopy	retro_nleu_1485 ,
Pongo abelii	ENSPPYG00000020545	1 retrocopy	retro_pabe_397,
Pan troglodytes	ENSPTRG00000023413	1 retrocopy	retro_ptro_228,