RetrogeneDB ID: retro_shar_625

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856823.1:739428..740092(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000010742
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HNRNPDL
• Ensembl ID: ENSSHAG00000013616
• Aliases: None
• Description: heterogeneous nuclear ribonucleoprotein D-like [Source:HGNC Symbol;Acc:5037]

Sequence

>retro_shar_625
GGCTCTAAGCAACGCGTCGGGACTCCCTCTCCGGGCCACCTGTCCCCAGCCTCCTCGGAAGACCTGCACGGACTTGACAA
CTTGGAGGAGCTCTCCCCCAACAAGAGCTCCCAAATCCGCGCGAGCGAGAGCGGGCAGGACGGCGGCAAAATGTTTATTG
GAGGTGTAAGCTGGGATGGGAGCCAGAAAGATCTCGTCGGATACCTGTTTGGTTTTGGAGTAGTCCTTGAAGTCAGCGCA
TTTAAAATGGATCCCCTCTCAGGGAAACTCGAGTGGTTTTGCATTTGTGCTTTTCAAAGATGCTTCCAATGATAAGGTCC
TGGAACTTAAAGAGCCCAAGCTGGATGACAAGTTGATAGACCTCAAATGGGCTAAAGCGAAAGGAGCTCTCCGAAAAAAA
GCATTTGTTGGTGGAGTGAACTCGGATATATCTGAAGAACAAATCAAAGAATACTTTGGAGCATTTGGAGGGATGGAACA
GATTGAACTCCTTATCCACCGAAAAGGAAATGAAAGAAGAGGATCTTGTTTCATCACATATACAGATGAAGAACCAGAAA
GAATGATTAGAAGTAGATATCATCAGCTTGTTTCTGGGAAGTGTGAAATCGAAGTTGCCCGGCCCAGAGATGTATACAGG
AAGCAACAGCAATAACAGGAGGGA

Alignment

ORF - retro_shar_625 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.48 %
• Parental protein coverage: 60.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GSIQRAAAATPSPRHLPPADSPAAMEDVNEYSNMEEFA--EGSKINASKNQQDDGKMFIGGLSWDTSKKD
          GS.QR....TPSP.HL....SPA..ED.....N.EE......S.I.AS...QD.GKMFIGG.SWD.S.KD
Retrocopy GSKQRVG--TPSPGHL----SPASSEDLHGLDNLEELSPNKSSQIRASESGQDGGKMFIGGVSWDGSQKD

Parental  LTEYLSRFGEVVDCT-IKTDPVTGR-SRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKEP
          L..YL..FG.V......K.DP..G..S.GF.FVLFKDA...DKVLELKE.KLD.KLID.K.AKA.KG...
Retrocopy LVGYLFGFGVVLEVSAFKMDPLSGK>SSGFAFVLFKDASN-DKVLELKEPKLDDKLIDLKWAKA-KGALR

Parental  PKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTKTNERRGFCFITYTDEEPVKKLLENRYHQIGSG
          .K..FVGG...D.SEEQIKEYFGAFG..E.IEL....K.NERRG.CFITYTDEEP.......RYHQ..SG
Retrocopy KK-AFVGGVNSDISEEQIKEYFGAFGGMEQIELLIHRKGNERRGSCFITYTDEEP-ERMIRSRYHQLVSG

Parental  KCEIKVAQPKEVYRQQQQQQKG
          KCEI.VA.P..VYR.QQQ.Q.G
Retrocopy KCEIEVARPRDVYRKQQQ*QEG

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_625 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 8 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003887	7 retrocopies	retro_dnov_1175, retro_dnov_1182, retro_dnov_144, retro_dnov_1603, retro_dnov_31, retro_dnov_723, retro_dnov_930,
Monodelphis domestica	ENSMODG00000011916	6 retrocopies	retro_mdom_1496, retro_mdom_1789, retro_mdom_1951, retro_mdom_2017, retro_mdom_546, retro_mdom_981,
Otolemur garnettii	ENSOGAG00000002501	4 retrocopies	retro_ogar_2717, retro_ogar_2791, retro_ogar_437, retro_ogar_693,
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	ENSSTOG00000013979	1 retrocopy	retro_itri_1177,
Tupaia belangeri	ENSTBEG00000002817	7 retrocopies	retro_tbel_2079, retro_tbel_2283, retro_tbel_2608, retro_tbel_2874, retro_tbel_3344, retro_tbel_4302, retro_tbel_4405,