RetrogeneDB ID: retro_tsyr_1480

Retrocopy location

• Organism: Tarsier (Tarsius syrichta)
• Coordinates: scaffold_459450:189..757(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSTSYG00000012949
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_tsyr_1480
TCCAGGGTCTTTGGATTTGTCACACCTGCCACCATGGAAAAGGTAGATGCAGCCATGAATACAAGGCCACACCGGGCAGA
CGGAAGACTTATGGAACCAAAGAGAGCTGTCGCAAGAGAATATTCTCAAAGACCAAGTGCCCACTTCACTGTGAAAAAGA
TATTTGTTGGTGGCATTAAAGAAGACACAGAAGCACATCACCTAAGAGATTATTTTGAACAGTATGGGAAAGCTGAAGTG
ATGAAAATCATGACTGACCAAGGCAGTGGCAAGGCAGTGACTGTAATCTTTGACAGCCATGACTCCGTGGACAAAATCAT
CATTCAGAAATACCACACTGTGAATGGCCACAACTGTAAAGTAAAGAAAGACCTGTGGAAGCGAGATGGCTTGTGCTTCA
TCCAGCCAAAGAAGTCGAAGTGGTTCTGGAAACTTTGGTGGTGGTGGACGTGGTTTTAGTGAGAATAACAACTTTGGTCA
AGGAGGAAACTTCTGTAGTCATGGTGGCTTTGGTGACAGCCATGGTGGTGGTGGATATGGTGGCAGTGGGCATGACTATA
ATGGATTT

Alignment

ORF - retro_tsyr_1480 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.88 %
• Parental protein coverage: 51.85 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SRGFGFVTYSCVEEGDAAMCARPHKVDGRVVEPKRAVSREDSVKPGAHLTVKKIFVGGIKEDTEEYNLRD
          SR.FGFVT....E..DAAM..RPH..DGR..EPKRAV.RE.S..P.AH.TVKKIFVGGIKEDTE...LRD
Retrocopy SRVFGFVTPATMEKVDAAMNTRPHRADGRLMEPKRAVAREYSQRPSAHFTVKKIFVGGIKEDTEAHHLRD

Parental  YFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHTINGHNCEVKKALSKQE-MQSAGSQ
          YFE.YGK.E....M.D..SGK......V.FD.HD.VDKI..QKYHT.NGHNC.VKK.L.K........SQ
Retrocopy YFEQYGKAEVMKIMTDQGSGKA---VTVIFDSHDSVDKIIIQKYHTVNGHNCKVKKDLWKRD>ACASSSQ

Parental  RGRGGGSGNFMGRGGNFGGGGGNFGRGGNFGGRGGYGGGGGGSRGSYGGGDGGYNGF
          R.R..GSGNF.G.G..F.....NFG.GGNF...GG.G...GG..G.YGG....YNGF
Retrocopy RSR-SGSGNFGGGGRGF-SENNNFGQGGNFCSHGGFGDSHGG--GGYGGSGHDYNGF

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_1480 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 16 parental genes, and 46 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Ficedula albicollis	ENSFALG00000003215	1 retrocopy	retro_falb_15,
Gallus gallus	ENSGALG00000009250	1 retrocopy	retro_ggal_10,
Monodelphis domestica	ENSMODG00000019803	1 retrocopy	retro_mdom_1590,
Mustela putorius furo	ENSMPUG00000014103	6 retrocopies	retro_mputfur_1141, retro_mputfur_1336, retro_mputfur_1545, retro_mputfur_603, retro_mputfur_674, retro_mputfur_779,
Oryctolagus cuniculus	ENSOCUG00000002743	2 retrocopies	retro_ocun_994, retro_ocun_995,
Otolemur garnettii	ENSOGAG00000025948	3 retrocopies	retro_ogar_1685, retro_ogar_3010, retro_ogar_3175,
Pongo abelii	ENSPPYG00000012967	1 retrocopy	retro_pabe_450,
Pelodiscus sinensis	ENSPSIG00000003011	1 retrocopy	retro_psin_16,
Pan troglodytes	ENSPTRG00000012676	5 retrocopies	retro_ptro_1059, retro_ptro_2430, retro_ptro_2966, retro_ptro_683, retro_ptro_872,
Rattus norvegicus	ENSRNOG00000001556	11 retrocopies	retro_rnor_1510, retro_rnor_1665, retro_rnor_1869, retro_rnor_2053, retro_rnor_2659, retro_rnor_2669, retro_rnor_2713, retro_rnor_2776, retro_rnor_2809, retro_rnor_348, retro_rnor_959,
Tarsius syrichta	ENSTSYG00000010395	3 retrocopies	retro_tsyr_1092, retro_tsyr_2070, retro_tsyr_269,
Tarsius syrichta	ENSTSYG00000012949	2 retrocopies	retro_tsyr_1480 , retro_tsyr_2122,
Tursiops truncatus	ENSTTRG00000014225	3 retrocopies	retro_ttru_1459, retro_ttru_675, retro_ttru_9,
Xenopus tropicalis	ENSXETG00000001806	1 retrocopy	retro_xtro_11,
Xiphophorus maculatus	ENSXMAG00000000439	1 retrocopy	retro_xmac_2,