RetrogeneDB ID: retro_shar_107

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841445.1:747127..748459(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000010782
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000014628
• Aliases: None
• Description: None

Sequence

>retro_shar_107
ATGTCGATCCCGTGGCTCTTCACCAAGAAGCTCCCCATTCATTGCATGGCTGGGGCCGTCCCGGTTTGCAATGAGAAGGG
GGAGATTTCAATGGAGAAAGTGAAGGTGAAACGTTATATATCGGGGAGGAGACCAGACTACGCCCCTAGGGAGTCCTCAG
ATGAGGAGGATGAGGAATTTCAATTCCTTAAGAAAGCCAAGGAGCAAGAAGCAGAGCCCGAGGAACAGGAAGAGGATTTA
CCCGGCGATCCCCGGCTTCGGCGTCTACAAAACCGCATCAAGGAAGATGCGGAAGAAAGGTTGGCCCGCCATCGGGAAAT
AATAGAGCCTGAAGTGATAGGAAAAAGTGATTCTGAAGAAGCAGGAGATGCAAGACAAATGGAGCGAGAGGACAGTGGGG
AGGAAGAGGAGGAAGAAATTGAGGAGGAAATTGAGGAGGAAATTGAGTGGCGGCGGGCCATGATGCGAAAGCGAGCACAA
GAAAGGAAAAATGAAGAAGTGGAAGTCATGGAAGTGGAAGATGAAGAGCATTCTGGGGAGGAATCCGAATCTGAATCCGA
GTCGGAGTATGAAGAATATATGGACAGTGAGGATGAAGTGGAAGTCCGTCTCAAGCCAGTCTTCATTCGGAAGAAGGACC
GGATAACAGTTCAAGAGCGTGAGGCGGAAGCACGGAAGCAGAAGGAGTTGGAGCAGGAGGCAGAACGTCTGGCTGAGGAG
AGGCGCAAATATACTCTCAAGATCGTGGAAGAGGAGACAAAGAAAGAACTAAGCGAAAACAAACGTTCCGTGGCTGCCCT
AGATGCGCTCAATTCAGATGACGAGAACGATGAGGAGGAATATGAGGCATGGAAAGTTCGGGAGTTAAAAAGAATCAAAC
GGGACAGAGAGGAACGGGAAGCGAGGGCGAAGGAGAAAGCAGACACTGAACGTATACGAAATCTGCCGGAAGAGGAAAGA
CGAGCTGAATTCCGAGCAAATGACAGAGTTATTACCAACAAAGCTGTCAAGGGCAAATACAAGTTCTTGCAGAAGTACTA
TCACCGGGGTGCTTTCTTTATGGATAAAGATGAAGAAATATACAAGAGAGATTTTAGTGTTCCCACCCTGGAGGATCATT
TCAATAAGACTATTCTTCCCAAAATTATGCAGGTTAAGAACTTTGGACGGTCAGGCAGAACCAAATATACCCATCTTGTG
GACCAAGATACCACTTCCTTTGATTCAGCTTGGGGTCGAGAGAATGCCCAAAATACCAGGTTCTTCACAGAAAAAGCAGC
TGGGGTACGAAATGTATTTGAAAGGCCATCTGCCAGGAAGAAGAAGAAAACT

Alignment

ORF - retro_shar_107 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.46 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSVPSALMKQPPIHSTAGAVPVRNEKGEISMEKVKVKRYVSGKRPDYAPMESSDEEDEEFQFIKKAKEQE
          MS.P....K..PIH..AGAVPV.NEKGEISMEKVKVKRY.SG.RPDYAP.ESSDEEDEEFQF.KKAKEQE
Retrocopy MSIPWLFTKKLPIHCMAGAVPVCNEKGEISMEKVKVKRYISGRRPDYAPRESSDEEDEEFQFLKKAKEQE

Parental  AEPEEQEEDSPSDPRLRRLQNRINEDVEERLARHRKIVEPEVVGESDSEVEGDARRMEREDSSEEEEEEI
          AEPEEQEED.P.DPRLRRLQNRI.ED.EERLARHR.I.EPEV.G.SDSE..GDAR.MEREDS.EEEEEEI
Retrocopy AEPEEQEEDLPGDPRLRRLQNRIKEDAEERLARHREIIEPEVIGKSDSEEAGDARQMEREDSGEEEEEEI

Parental  DD---EEIEWRRGMMRQRAQERKNEEMEVMEVEDEGHSGEESESESE--YEEYTDSEDEMEPRLKPVFIR
          .....EEIEWRR.MMR.RAQERKNEE.EVMEVEDE.HSGEESESESE..YEEY.DSEDE.E.RLKPVFIR
Retrocopy EEEIEEEIEWRRAMMRKRAQERKNEEVEVMEVEDEEHSGEESESESESEYEEYMDSEDEVEVRLKPVFIR

Parental  KKDRVTVQEREAEALKQKELEQEAKRLAEERRKYTLKIVEEETKKELEENKRSLAALDALNTDDENDEEE
          KKDR.TVQEREAEA.KQKELEQEA.RLAEERRKYTLKIVEEETKKEL.ENKRS.AALDALN.DDENDEEE
Retrocopy KKDRITVQEREAEARKQKELEQEAERLAEERRKYTLKIVEEETKKELSENKRSVAALDALNSDDENDEEE

Parental  YEAWKVRELKRIKRDREDREAIEKEKAEIERMRNLTEEERRAELRANGKVITNKAVKGKYKFLQKYYHRG
          YEAWKVRELKRIKRDRE.REA..KEKA..ER.RNL.EEERRAE.RAN..VITNKAVKGKYKFLQKYYHRG
Retrocopy YEAWKVRELKRIKRDREEREARAKEKADTERIRNLPEEERRAEFRANDRVITNKAVKGKYKFLQKYYHRG

Parental  AFFMDEDEEVYKRDFSAPTLEDHFNKTILPKVMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGQESAQNTK
          AFFMD.DEE.YKRDFS.PTLEDHFNKTILPK.MQVKNFGRSGRTKYTHLVDQDTTSFDSAWG.E.AQNT.
Retrocopy AFFMDKDEEIYKRDFSVPTLEDHFNKTILPKIMQVKNFGRSGRTKYTHLVDQDTTSFDSAWGRENAQNTR

Parental  FFKQKAAGVRDVFERPSAKKRKTT
          FF..KAAGVR.VFERPSA.K.K.T
Retrocopy FFTEKAAGVRNVFERPSARKKKKT

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_107 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000013870	1 retrocopy	retro_dord_22,
Myotis lucifugus	ENSMLUG00000013000	2 retrocopies	retro_mluc_1384, retro_mluc_2298,
Mus musculus	ENSMUSG00000048222	2 retrocopies	retro_mmus_1147, retro_mmus_2346,
Mus musculus	ENSMUSG00000068479	2 retrocopies	retro_mmus_2386, retro_mmus_2638,
Otolemur garnettii	ENSOGAG00000010206	1 retrocopy	retro_ogar_1784,
Rattus norvegicus	ENSRNOG00000015984	1 retrocopy	retro_rnor_83,
Sarcophilus harrisii	ENSSHAG00000014628	1 retrocopy	retro_shar_107 ,
Ictidomys tridecemlineatus	ENSSTOG00000006967	2 retrocopies	retro_itri_1105, retro_itri_1494,
Tupaia belangeri	ENSTBEG00000005050	2 retrocopies	retro_tbel_3001, retro_tbel_3246,