RetrogeneDB ID: retro_shar_527

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849809.1:571537..572200(+)
• Located in intron of: ENSSHAG00000009039

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_527
GACAAGGTCTTGGAGTTTAAAGAACACAAGCTAGGTAACAAATTGATAGACCACAAAAGGGCCAGAGTCTTAAAAGGAAA
GGATCCCCCCCAAAAAAATATTTGTCAGTGGAATGAGTTCAATTATGTCTGAAGAACAAATCAAAATTATTTTGGAGTAT
TTGGAAAGATTTGGAAAAAGCACTAAAATAGTGCTCTTCCTAAGGACACAAAAATAAATGTAAAAAGGATTTTATTTTAT
TACATATACAGATGAGAATCAGCAAAAAAAATTTATTAGAAAACAGATATCATCAGATTGGTTCTGGGAAGTGTGAAATC
ACAATCCAAAGAGGAATACAGGTAGCAACAGCAACAGCAACGATAGAAACATGGGAGGGGTGTTGCAGCTGGTAATAGAG
ATGGGAGTAGGAATCATGGCTGAGGTCAGGGCCAAAACTGGAATCAAGAATTTAATAATTATTATGATTGAGGATGTGGA
AATTACAATCATGCCTATCGTAGTGATAAAAAATATAGGGATAATGATGGATATGATTACACTGGGTATAATTATGCTAA
CTATGGATATAGAGGGAAATATGCAAACTATAGTAGTCAACAAAATATGTATAGCAAAGCATTCCAATGGGGTGATAATT
ACCAAAACAATTATCAGCCATAT

Alignment

ORF - retro_shar_527 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.71 %
• Parental protein coverage: 58.13 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DKVLELKEHKLDGKLIDPKRAKALKGKEPP-KKVFVGGLSPDTSEEQIK---EYFGAFGEIENIELPMDT
          DKVLE.KEHKL..KLID.KRA..LKGK.PP.KK.FV.G.S...SEEQIK...EY...FG....I.L...T
Retrocopy DKVLEFKEHKLGNKLIDHKRARVLKGKDPP>KKIFVSGMSSIMSEEQIKIILEYLERFGKSTKIVLFLRT

Parental  KTNERRGFCFITYTDEEPVKK-LLENRYHQIGSGKCEIKVAQPKEV-YRQQQQQQKGGRGAAAGGRGGTR
          ......GF.FITYTDE......LLENRYHQIGSGKCEI.......V...QQ.Q..K.GRG.AAG.R.G.R
Retrocopy QK*M*KGFYFITYTDENQXXX>LLENRYHQIGSGKCEITIQRGIQV>QQQQ-QR*KHGRGVAAGNRDGSR

Parental  GRGRGQGQNWNQGFNNYYDQGYGNYNSAYGGDQNYSGYGGYDYTGYNYGNYGYGQGYADYSGQQSTYGKA
          ..G.GQGQNWNQ.FNNYYD.G.GNYN.AY..D..Y....GYDYTGYNY.NYGY...YA.YS.QQ..Y.KA
Retrocopy NHG*GQGQNWNQEFNNYYD*GCGNYNHAYRSDKKYRDNDGYDYTGYNYANYGYRGKYANYSSQQNMYSKA

Parental  SRGGGNHQNNYQPY
          ...G.N.QNNYQPY
Retrocopy FQWGDNYQNNYQPY

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_527 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,