RetrogeneDB ID: retro_tbel_2891

Retrocopy location

• Organism: Treeshrew (Tupaia belangeri)
• Coordinates: scaffold_122475:176368..177163(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSTBEG00000002910
• Aliases: None
• Description: cysteine and histidine-rich domain (CHORD) containing 1 [Source:HGNC Symbol;Acc:14525]

Sequence

>retro_tbel_2891
GGTTGTACAAAAGGTAGGCATAATAGTGAGAAACCACCTGAGCCAGTCAAACCTGAAGTCAAGACTACTGAAAAGAAAGA
GGCATCTGAATTGAAACCCAAATTCCAGGAGCACATCATTCAAGGCCCTAAGGCAGTAGAGGCAATAAAAAGGCTAAGTC
CAGATGAATCAATGACAATTTTGGAATTAAAAGTATCTGCTTCCCTAAAACAAGCACTTGATAAACTTAAACTGCCATCT
GGGAATGAAGAAGACAAGAAAGAAGCAGACAGTGATGAAATTAAGATTGGGACCTCATGTAAAAATGGAGGGTGTTCCAA
GACATACCAAGGTCTACAGAGTTTAGAAGAAGTCTGCATATATCACCCCGGAGTACCTATTTTCCATGAGGGGATGAAAT
ACTGGAGATGTTGTAGAAGAAAGACTTCTGATTTTAATACATTCTTATCCCAAGAAGGCTGTACAACAGGGAAACACATG
TGGACTAAAAAGGATGATGGGAAAAAAGTTGTTTCATGTAGACATGACTGGCATCAGACTGGAGGTGAAGTCACCATTTC
AGCATATGCTAAAAATTCACTTCCGGAACTCAGCCAAGTAGAAGCAAATAGTACATTGTTAAATGTACACATTGTTTTTG
AAGGAGAAAAGGAATTTCATCAAAATGTGAGATTATGGGGTGTGATTGATGTAAAGTGGAGTTATGTAACTATGACTGCA
ACAAAGATTGAGATCACCATGAGAAAAGCTGAACTCATGAAGTGGGCAAGCCTTGAACTGCCTGCAGCCAAAAAG

Alignment

ORF - retro_tbel_2891 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.83 %
• Parental protein coverage: 82.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GCTKGRHNSEKPPEPVKPEVKTTEKKEASELKPKFQEHIIQAPKPVEAIKRPSPDEPMTNLELKVSASLK
          GCTKGRHNSEKPPEPVKPEVKTTEKKEASELKPKFQEHIIQ.PK.VEAIKR.SPDE.MT.LELKVSASLK
Retrocopy GCTKGRHNSEKPPEPVKPEVKTTEKKEASELKPKFQEHIIQGPKAVEAIKRLSPDESMTILELKVSASLK

Parental  QALDKLKLSSGNEEDKKEEDSDEIKIGTSCKNGGCSKTYQGLQSLEEVCVYHSGVPIFHEGMKYWSCCRR
          QALDKLKL.SGNEEDKKE.DSDEIKIGTSCKNGGCSKTYQGLQSLEEVC.YH.GVPIFHEGMKYW.CCRR
Retrocopy QALDKLKLPSGNEEDKKEADSDEIKIGTSCKNGGCSKTYQGLQSLEEVCIYHPGVPIFHEGMKYWRCCRR

Parental  KTSDFNTFLSQEGCTTGKHMWTKKDDGKKVVSCRHDWHQTGGEVTISVYAKNSLPELSQVEANSTLLNVH
          KTSDFNTFLSQEGCTTGKHMWTKKDDGKKVVSCRHDWHQTGGEVTIS.YAKNSLPELSQVEANSTLLNVH
Retrocopy KTSDFNTFLSQEGCTTGKHMWTKKDDGKKVVSCRHDWHQTGGEVTISAYAKNSLPELSQVEANSTLLNVH

Parental  IVFEGEKEFHQNVRLWGVIDVKRSYVTMTATKIEITM-KAEPMQWSL--LPAAKK
          IVFEGEKEFHQNVRLWGVIDVK.SYVTMTATKIEITM.KAE.M.W....LPAAKK
Retrocopy IVFEGEKEFHQNVRLWGVIDVKWSYVTMTATKIEITMRKAELMKWASLELPAAKK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Tupaia belangeri was not studied using RNA-Seq expression data.

ChIP-Seq

Tupaia belangeri was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_tbel_2891 retrocopy.

TSS

Tupaia belangeri was not studied using FANTOM5 data.

Lab

retro_tbel_2891 was not experimentally validated.

Homology

Retrocopy orthology:

Tupaia belangeri 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 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000903	4 retrocopies	retro_cjac_2220, retro_cjac_2927, retro_cjac_4147, retro_cjac_815,
Echinops telfairi	ENSETEG00000013104	2 retrocopies	retro_etel_1713, retro_etel_1860,
Felis catus	ENSFCAG00000019389	1 retrocopy	retro_fcat_137,
Homo sapiens	ENSG00000110172	3 retrocopies	retro_hsap_1452, retro_hsap_1903, retro_hsap_2252,
Gorilla gorilla	ENSGGOG00000027396	3 retrocopies	retro_ggor_1117, retro_ggor_1118, retro_ggor_1679,
Loxodonta africana	ENSLAFG00000017340	1 retrocopy	retro_lafr_401,
Macaca mulatta	ENSMMUG00000005209	2 retrocopies	retro_mmul_1024, retro_mmul_1923,
Nomascus leucogenys	ENSNLEG00000007079	5 retrocopies	retro_nleu_1085, retro_nleu_1232, retro_nleu_1320, retro_nleu_752, retro_nleu_981,
Oryctolagus cuniculus	ENSOCUG00000014147	1 retrocopy	retro_ocun_1595,
Otolemur garnettii	ENSOGAG00000003523	1 retrocopy	retro_ogar_2724,
Pongo abelii	ENSPPYG00000003764	5 retrocopies	retro_pabe_1199, retro_pabe_1554, retro_pabe_1734, retro_pabe_1959, retro_pabe_461,
Pan troglodytes	ENSPTRG00000004164	3 retrocopies	retro_ptro_1253, retro_ptro_1595, retro_ptro_988,
Tupaia belangeri	ENSTBEG00000002910	1 retrocopy	retro_tbel_2891 ,
Tarsius syrichta	ENSTSYG00000004205	1 retrocopy	retro_tsyr_1581,