RetrogeneDB ID: retro_shar_518

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849754.1:770846..771393(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HNRNPA3
• Ensembl ID: ENSSHAG00000018255
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein A3 [Source:HGNC Symbol;Acc:24941]

Sequence

>retro_shar_518
AGAGAACACTTTGAAAACATTTTCACAGATTGTGTGGTGATGAGAGATTCCCCAAACAAAATGTTCCAGAGGCTATGGTT
TTGTGATTTATCCTTGTGTAAAAGAGGTAAAAGCAACAATGTGTGCTCAGCCACATAAGGTAGATGGGCATGTAATGGAA
CCAAAGAGAGCTGTTTCTAGAGAGGGTTCTGTAAAACCTCATTCACATCTAACCAGGAAGATAATGTTTGCCGGTAGTAT
TAAAGAAGATATAGAAGAATAAAATTTAAGAGACTATTTTTCGAAAAGTATGGCAATTTTGAAACTCTAGAAGTTATGGA
AGATTGACAGAGTAGAAAAAAGAGAATTTACTTTTGTAATTTTTTATAATCATAATACAAGAGACAAAATTATTCAGAAA
TAACATACTATTAATGGGCATAATTGTAAAGTGAAAAGGCCCTTATGGAGTAAGAGGTGTAAGCTTCTGGCTTACAAAGA
GGTCATAGTGATGGCTCAGGTCATTTCCCACTCAGATGGTGTACTGCTTGAGCGTGGTGGTGGAAAC

Alignment

ORF - retro_shar_518 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.11 %
• Parental protein coverage: 57.1 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  REHFEKWGTLTDCVVMRD-PQTKRSRGFGFVTYSCVEEVDAAMCARPHKVDGRVVEPKRAVSREDSVKPG
          REHFE.....TDCVVMRD.PQTK.SRG.GFV.Y.CV.EV.A.MCA.PHKVDG.V.EPKRAVSRE.SVKP.
Retrocopy REHFEN--IFTDCVVMRD>PQTKCSRGYGFVIYPCVKEVKATMCAQPHKVDGHVMEPKRAVSREGSVKPH

Parental  AHLTVKKIFVGGIKEDTEEYNLRDYFEKYGKIETIEVMEDRQSGKKRGFAFVTFDDHDTVDKIVVQKYHT
          .HLT.K..F.G.IKED.EE.NLRDYF.K...I.............KR.F.FV.F..H.T.DKI..QK.HT
Retrocopy SHLTRKIMFAGSIKEDIEE*NLRDYFSKSMAILKL*KLWKIDRVEKREFTFVIFYNHNTRDKI-IQK*HT

Parental  INGHNCEVK-KALSKQEMQSAGSQRGRGGGSGNFMGR-GGNFGGGGGN
          INGHNC.VK.KAL...E....G.QRG...GSG.F..R.G.....GGGN
Retrocopy INGHNCKVK<KALME*EV*ASGLQRGHSDGSGHFPLR>GVLLERGGGN

Legend:

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

Expression

RNA-Seq

Sarcophilus harrisii was not studied using RNA-Seq expression data.

ChIP-Seq

Sarcophilus harrisii was not studied using ChIP-Seq data.

EST

Sarcophilus harrisii was not studied using EST data.

TSS

Sarcophilus harrisii was not studied using FANTOM5 data.

Lab

retro_shar_518 was not experimentally validated.

Homology

Retrocopy orthology:

Sarcophilus harrisii 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 22 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011920	4 retrocopies	retro_amel_1407, retro_amel_557, retro_amel_715, retro_amel_765,
Bos taurus	ENSBTAG00000021580	8 retrocopies	retro_btau_1029, retro_btau_1310, retro_btau_1587, retro_btau_212, retro_btau_277, retro_btau_370, retro_btau_811, retro_btau_90,
Cavia porcellus	ENSCPOG00000004251	3 retrocopies	retro_cpor_1516, retro_cpor_1543, retro_cpor_65,
Felis catus	ENSFCAG00000012146	5 retrocopies	retro_fcat_1231, retro_fcat_572, retro_fcat_662, retro_fcat_677, retro_fcat_842,
Gorilla gorilla	ENSGGOG00000006130	6 retrocopies	retro_ggor_1001, retro_ggor_1197, retro_ggor_14, retro_ggor_1736, retro_ggor_576, retro_ggor_702,
Macaca mulatta	ENSMMUG00000001858	4 retrocopies	retro_mmul_1945, retro_mmul_2442, retro_mmul_386, retro_mmul_801,
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,
Mus musculus	ENSMUSG00000059005	6 retrocopies	retro_mmus_133, retro_mmus_1359, retro_mmus_1409, retro_mmus_210, retro_mmus_3635, retro_mmus_60,
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,
Otolemur garnettii	ENSOGAG00000028132	7 retrocopies	retro_ogar_1869, retro_ogar_1924, retro_ogar_2222, retro_ogar_2590, retro_ogar_3215, retro_ogar_600, retro_ogar_814,
Pongo abelii	ENSPPYG00000012967	1 retrocopy	retro_pabe_450,
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,
Sarcophilus harrisii	ENSSHAG00000013312	1 retrocopy	retro_shar_752,
Sarcophilus harrisii	ENSSHAG00000013616	3 retrocopies	retro_shar_297, retro_shar_527, retro_shar_625,
Sarcophilus harrisii	ENSSHAG00000018255	1 retrocopy	retro_shar_518 ,
Ictidomys tridecemlineatus	ENSSTOG00000025125	4 retrocopies	retro_itri_1444, retro_itri_1878, retro_itri_952, retro_itri_98,
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,