RetrogeneDB ID: retro_shar_598

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856722.1:129839..130205(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRSF9
• Ensembl ID: ENSSHAG00000005685
• Aliases: None
• Description: serine/arginine-rich splicing factor 9 [Source:HGNC Symbol;Acc:10791]

Sequence

>retro_shar_598
AGTCAGAAACAGAGCTGGAAGGCGAATCCATCCATCAATCAACTCACATCATCAGGCAGCTGACAGGATTGAAAGATCAC
ACAGGAGAAGCTGGTGGGGTGTGTCTTGCAGATGTTGTGCAGAAGGATGGCACAGGGGGTGGGTAAGTTTCTCTGCAACA
AAGATATGGAATACGCCCTGCATGTACTGAATGATTCCAAATTCCATTCTCATGAGGATGAAGCCTCTTTAATCAGAGTT
TATGCAGAAAAAAAAAAAAACACCACCAGTTATGGTTATTCCTGCTTTAGGTCAGGATCAAGGGGCCATGATTCTTCATA
CCGGAGCAGTAGCTCCCCAAACTACAGTTCTCCCTTTACATCCTAC

Alignment

ORF - retro_shar_598 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.26 %
• Parental protein coverage: 74.68 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRRSEYRVLVSGPGLPPSGSWQD-LKDHMREAGGVCYADV-QKDG-MGVVEFLRKEDMEYALRRLDDSKF
          S.........S...L..SGS.QD.LKDH..EAGGVC.ADV.QKDG..GV..FL...DMEYAL..L.DSKF
Retrocopy SQKQSWKANPSINQLTSSGS*QD<LKDHTGEAGGVCLADVVQKDG>QGVGKFLCNKDMEYALHVLNDSKF

Parental  RSHEGETSYIRVYPER---STSYGYSRSRSGSRGRDSPYQSRGSPYYTSPYAPY
          .SHE.E.S.IRVY.......TSYGYS..RSGSRG.DS.Y.S..SP.Y.SP...Y
Retrocopy HSHEDEASLIRVYAXXXXXTTSYGYSCFRSGSRGHDSSYRSSSSPNYSSPFTSY

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_598 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 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000012792	1 retrocopy	retro_btau_837,
Choloepus hoffmanni	ENSCHOG00000009241	1 retrocopy	retro_chof_1119,
Callithrix jacchus	ENSCJAG00000001187	1 retrocopy	retro_cjac_442,
Dasypus novemcinctus	ENSDNOG00000012598	2 retrocopies	retro_dnov_1555, retro_dnov_2648,
Homo sapiens	ENSG00000111786	1 retrocopy	retro_hsap_2530,
Macaca mulatta	ENSMMUG00000016494	1 retrocopy	retro_mmul_2154,
Nomascus leucogenys	ENSNLEG00000015661	1 retrocopy	retro_nleu_1931,
Otolemur garnettii	ENSOGAG00000003852	1 retrocopy	retro_ogar_2328,
Ochotona princeps	ENSOPRG00000004234	1 retrocopy	retro_opri_878,
Pongo abelii	ENSPPYG00000005031	1 retrocopy	retro_pabe_119,
Sarcophilus harrisii	ENSSHAG00000005685	1 retrocopy	retro_shar_598 ,
Sarcophilus harrisii	ENSSHAG00000015970	1 retrocopy	retro_shar_72,
Sus scrofa	ENSSSCG00000009906	1 retrocopy	retro_sscr_745,
Tupaia belangeri	ENSTBEG00000008499	1 retrocopy	retro_tbel_2602,
Tarsius syrichta	ENSTSYG00000006848	4 retrocopies	retro_tsyr_1432, retro_tsyr_1648, retro_tsyr_585, retro_tsyr_891,