RetrogeneDB ID: retro_tsyr_1581

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_498541:12..756(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHORDC1
• Ensembl ID: ENSTSYG00000004205
• Aliases: None
• Description: cysteine and histidine-rich domain (CHORD) containing 1 [Source:HGNC Symbol;Acc:14525]

Sequence

>retro_tsyr_1581
GAACCACCCGAGCCAGTCAAGTCTGAAGTCAAGACTATTGAGAAGAAAGAACTATCTGAATTGAAACCCAAATTTCAGGA
ATGTATCATTCAAGTCCCTAAGCCAGTAATAAATAAAGTAATAAATAGGCCAGGCCCAGATGAACCAATGACAAATTTGG
AATTTAAAATATCTGCCTCCCTAAAACAAGCACTTGATAATCTTAAACTGTCATCAAGAAAGAAAGATGAACACAATGAT
GAAATTAAGATTGGAACCTCATGAAAAAATGGAGGGTATTCAAAGATATATCAAGGTCCACAGAATCTAGAAGAAGTCTG
TGTGCATCATTCTGGAGTACCTATTTTCCATGAGAGGATGAAAGACTGGAGCTGCTGTAGAAGAAAAACTTCTGATTTTA
ATACATTCTTAGCTCAAGAAGGCTGTACAACAGGGAAGCACATATAGAATAAAAAGGATGCTGGGAAAAAAGTTGTTCCA
TGTAGACATGACTGGCATCAGACTGGGGGTGAAGTCACCGTTTCAGTATATGCAAAAAATTCACTTCCAGAACTTAGTTG
AGTAGAAGCAAATATTACATTGTTAAATGTGCACATTGTATTTGAAGGAGAAAAGGAATTTCATCAAAATGTGAAATTAT
GGGGTGTGATTGATGTAAAGGAAAGTTATGTAACTATGACTGCAACAAAGATTGAGCTCACCACAAGAAAAGGTGAACCT
ATGCAGTGGGCAAGCCTCAAACTG

Alignment

ORF - retro_tsyr_1581 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.92 %
• Parental protein coverage: 75.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KPPEPVKPEVKTSEKKELSELKPKFQEHIIQAPKPV--EAIKRPSPDEPMTNLELKISASLKQALDKLKL
          .PPEPVK.EVKT.EKKELSELKPKFQE.IIQ.PKPV....I.RP.PDEPMTNLE.KISASLKQALD.LKL
Retrocopy EPPEPVKSEVKTIEKKELSELKPKFQECIIQVPKPVINKVINRPGPDEPMTNLEFKISASLKQALDNLKL

Parental  SSGKEEDKKEEENDEIKIGTSCKNGGCSKTYQGPQSLEEVCVYHSGVPIFHEGMKYWSCCRRKTSDFNTF
          SS.K....K.E.NDEIKIGTS.KNGG.SK.YQGPQ.LEEVCV.HSGVPIFHE.MK.WSCCRRKTSDFNTF
Retrocopy SSRK----KDEHNDEIKIGTS*KNGGYSKIYQGPQNLEEVCVHHSGVPIFHERMKDWSCCRRKTSDFNTF

Parental  LAQEGCTTGKHMWTKKDAGKKVVPCRHDWHQTGGEVTISVYAKNSLPELSQVEANSTLLNVHIVFEGEKE
          LAQEGCTTGKH...KKDAGKKVVPCRHDWHQTGGEVT.SVYAKNSLPELS.VEAN.TLLNVHIVFEGEKE
Retrocopy LAQEGCTTGKHI*NKKDAGKKVVPCRHDWHQTGGEVTVSVYAKNSLPELS*VEANITLLNVHIVFEGEKE

Parental  FHQNVKLWGVIDVKRSYVTMTATKIEITMRKAEPMQWASLEL
          FHQNVKLWGVIDVK.SYVTMTATKIE.T.RK.EPMQWASL.L
Retrocopy FHQNVKLWGVIDVKESYVTMTATKIELTTRKGEPMQWASLKL

Legend:

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

Expression

RNA-Seq

Tarsius syrichta was not studied using RNA-Seq expression data.

ChIP-Seq

Tarsius syrichta was not studied using ChIP-Seq data.

EST

Tarsius syrichta was not studied using EST data.

TSS

Tarsius syrichta was not studied using FANTOM5 data.

Lab

retro_tsyr_1581 was not experimentally validated.

Homology

Retrocopy orthology:

Tarsius syrichta 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 ,