RetrogeneDB ID: retro_shar_297

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841253.1:363115..363842(-)
• Located in intron of: ENSSHAG00000007782

Retrocopy information

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

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_297
CATTTCAAATCCAGTTTCATATAAACAGCTATCATTGTGACTCTGTTTCCTTGACACTTGCCCTCAGCTGACAGCCCTGC
CATCTGAGGGGACATGAATGAGTAGAGTAGCATAGACTTCAGCTGAAGGGTCCAAAATCAGCATGAACAAAAATACACAG
GACCTTGCTAAAATATTTTTTGGAAGGCTAAGCTGGGATACAAGCAAGAAAGAACTGATCAATTACTTCTCTTGTTTTGG
CAAGGTTGTAGGCTATATAATTAAAATGAATCTAGTGACTGGAAGATCATAGCAATTTGGATTTGTGCTTTTCAGACATT
CTCTCAGTGCTGACAGGGTCCAAGAATTTAAAGAAAACATAGAGGATAGCAAATGGATAGACTTCTAAATGGCCAAAGCT
TTAAAATGATAGGATCCCCACCCCCCAAAAAAGTATTTTGGAATAAATACATCTGAATAATTAATCAAAAAATATTTTAG
AACATTTGATAAGACTGAGAATGTTGGATTTTCTATGCACAAAAAATGTGAATAAAAAAAGATTCTATTTTATTACATAT
ATAGATGAAAAAGCATTTAATGAAATTATTAGAAAACAGATATCATCAAATTGATTATGGGAAGTGTACAATTTAAAATT
AGACATCCCAAAGAAATATGCAAGCAACAACAGAAAGGAAGGACGGGTGTTGCAGCTGGTGGACTATATGATATTACAGG
TCAGGGT

Alignment

ORF - retro_shar_297 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.17 %
• Parental protein coverage: 66.13 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  HFKSGSIQRAAAATPSPRHLPPADSPAAMEDVNEYSNMEEF-AEGSKINASKNQQDDGKMFIGGLSWDTS
          HFKS..I..A...T..P.HLP.ADSPA...D.NE.S....F.AEGSKI...KN.QD..K.F.G.LSWDTS
Retrocopy HFKSSFI*TAIIVTLFP*HLPSADSPAI*GDMNE*SSI-DF>AEGSKISMNKNTQDLAKIFFGRLSWDTS

Parental  KKDLTEYLSRFGEVVDCTIKTDPVTGRSRGFGFVLFKDAASVDKVLELKEHKLDGKLIDPKRAKALKGKE
          KK.L..Y.S.FG.VV...IK...VTGRS..FGFVLF....S.D.V.E.KE...D.K.ID...AKALK...
Retrocopy KKELINYFSCFGKVVGYIIKMNLVTGRS*QFGFVLFRHSLSADRVQEFKENIEDSKWIDF*MAKALK**D

Parental  P-PKKVFVGGLSPDTSEEQIKEYFGAFGEIENIELPMDTK-TNERRGFCFITYTDEEP-VKKLLENRYHQ
          P.P.K...G.....TSE..IK.YF..F...EN....M..K..N..R.F.FITY.DE.....KLLENRYHQ
Retrocopy PHPPKKYFG---INTSE*LIKKYFRTFDKTENVGFSMHKK>VNKKR-FYFITYIDEKA>LMKLLENRYHQ

Parental  IGSGKCEI-KVAQPKEVYRQQQQQQKGGRGAAAGGRGGTRGRG
          I..GKC.I.K...PKE...QQQ...KG..G.AAGG.....G.G
Retrocopy IDYGKCTI>KIRHPKEICKQQQ---KGRTGVAAGGLYDITGQG

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_297 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,