RetrogeneDB ID: retro_shar_445

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL847109.1:1301..3263(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000017091
• Aliases: None
• Description: None

Sequence

>retro_shar_445
AAACTCAACCATGATAGCATTGTGAAAGTATTTTAAATTCTTGGTCCCAGTGGAAGTCAGTTAACAGATGATGTGGGTTC
TCTGACAGAACTGAACAGTCTTTACATTGTTCAGGAGTACATGGAGACAGACGTGGCTAATCTGCTAAAGCAGGGCCCTT
TGCTGGAGGAGCATACCAGGCTTTTCATGTATCAGCTGCTACGTGGGCTAAAGTATATTCATTCTGCAAATGTACTGCAC
AGAGATCTCAAACCAGCTAATCTTTTCATTAATACTGAAGACTTGGTGCTGAAGATATGTGACTTTGGTAATGCCTGGAT
TATGAATCCCCATTATTCACATAAAAGTCATCTTTCTGAAGGATTGGTTACTAAATGGTACAGATCTCCAGGACTTTTAC
TTTCTTCCAATAATTACAGTAAAGCCATTGACATGTGGGATGCAGGATGCATCTTTGCTGATATGCTGACTGGAAAAACC
TTCTTTGCAGGTGCACAGAACTTGAACAAATGCAGCTGATTTTAGAATCTAATTCTATTGTACATGAGGAATATCGTCAG
GAGCTTCTCAGTGTAATCCCAGTTTATATATATATAAAAATGATATGATTGAACCACAAAAACCCTTAATTCAGATGCTT
CCAGGAATTAATTGTGAAGCACTGGACTTCCTGGAGCAAATTTTGACATTTAGTCCTATGAATCAATTGACAGCAGAAGA
AGCTCTGTCCCATCCTTATATGAGCATTTATTCCTTTCCAATGGATGAACCAATTTCAAGCCATCCTTTTTACATTGAAA
ATGAAAATGATGATATTTTGCTCATGGATGAAACTCATAGTCACATTTATAATTGGGAGAGGTAACATGATTATCAATTT
TCATACCATGACTGGCCTATACCCAACAATTTTGATATTGATAAAGTTCAGCATGACCCAAGGACTCTTTCTGATGTCAC
TGATGAAGAGGAAGTACAAGAAGATCCTCAAAAATATTTCGATGGAGATCATGAAAAGTCTCTACAGGATCCTGCCTTTG
ATACCCATTTCTCTACTGAGCCTTGTTGGCAGTATTCAGATCATCATGAAAATAAGTATTGTGATCTAGAATGCAGCCAC
ACTTGTAACTACAAAATGAGATCATCATGATATTTAGATAACTTAGTTTGGAGAGAGAGTGAAGTTAACCATTACTATGA
ACTCAAACTTATTATAGATCTTTCCAATTGGAAAGAACAAAGCAAAGAAAAATATGACAAGAAAGGCAAGTCAAAATGTG
AAAGGAATGGATTGGTTAAAACTCAAATAACTCCTGAGGAAGCATCACAGCAACTGGTTGAAAAAGAAAGGGAGAAGAAT
CAAAGATTTAACTTTTATTCCTTTATTGCAGGAACTATTCAACTTAGTTCACAACATGAGTCTACTGATGTTGTTAATAA
ATTAAATGACTTGAATAGCTCAGTGACCCAACTAGAATTGAAAACTTTGATATCAAAGTCAGTAAGCCGGGAAAAGCAAG
AAAAAGGAATGGCAAATTTAGTACAGTTAGAAGCTTTGTATCAGTCTTCTTGGGAAAGTCAGTATGTAAGTGGTGGGGAG
AAATGTTTTCTCAAAGAACAGTTTTGTTGTGAAGTAAGAAAGGATGAGCAAATTAAGAAGGAAAACACATACACTAATTA
CTTGGACAAGTTCTTTAGCAGGCAAGAAGATACTGAAATGCTAGAAACTGATCCAGTAGAGGATTGCAAGTTTGGGAAAA
GAGAAAGTGAGGAGGGTTTTCTTAACAATAGGAGGAGTTCCTCATTTTCCTCAAGCAGTTTGAGTCAAAAGGTATCTCAC
AGTTTCATAGTCCAGCTGATTCACCATTTAAATAACTATAGGCCACATTAATACCTTCTGCTATGAAATCTTCTCCCCAG
ATTCCTCCTAAAACACATAGCAGCATTTTGAAATATCTGAAC

Alignment

ORF - retro_shar_445 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.17 %
• Parental protein coverage: 90.3 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  RLDHDNIVKVFEILGPSGSQLTDDVGSLTELNSVYIVQEYMETDLANLLEQGPLLEEHARLFMYQLLRGL
          .L.HD.IVKVF.ILGPSGSQLTDDVGSLTELNS.YIVQEYMETD.ANLL.QGPLLEEH.RLFMYQLLRGL
Retrocopy KLNHDSIVKVF*ILGPSGSQLTDDVGSLTELNSLYIVQEYMETDVANLLKQGPLLEEHTRLFMYQLLRGL

Parental  KYIHSANVLHRDLKPANLFINTEDLVLKIGDFGLARIMDPHYSHKGHLSEGLVTKWYRSPRLLLSPNNYT
          KYIHSANVLHRDLKPANLFINTEDLVLKI.DFG.A.IM.PHYSHK.HLSEGLVTKWYRSP.LLLS.NNY.
Retrocopy KYIHSANVLHRDLKPANLFINTEDLVLKICDFGNAWIMNPHYSHKSHLSEGLVTKWYRSPGLLLSSNNYS

Parental  KAIDMWAAGCIFAEMLTGKTLFAGAH-ELEQMQLILESIPVVHEEDRQELLSVIPV--YIK-NDMTEPHK
          KAIDMW.AGCIFA.MLTGKT.FAGA..ELEQMQLILES...VHEE.RQELLSVIPV..YIK.NDM.EP.K
Retrocopy KAIDMWDAGCIFADMLTGKTFFAGAQ<ELEQMQLILESNSIVHEEYRQELLSVIPVYIYIK<NDMIEPQK

Parental  PLIQLLPGISREALDFLEQILTFSPMDRLTAEEALSHPYMSIYSFPMDEPISSHPFHIEDEVDDILLMDE
          PLIQ.LPGI..EALDFLEQILTFSPM..LTAEEALSHPYMSIYSFPMDEPISSHPF.IE.E.DDILLMDE
Retrocopy PLIQMLPGINCEALDFLEQILTFSPMNQLTAEEALSHPYMSIYSFPMDEPISSHPFYIENENDDILLMDE

Parental  THSHIYNWERYHDCQFSDHDWPIHNNFDIDEVQRDPRALSDVTDEEEVQVDPRKYLDGDREKYLKDPAFD
          THSHIYNWER.HD.QFS.HDWPI.NNFDID.VQ.DPR.LSDVTDEEEVQ.DP.KY.DGD.EK.L.DPAFD
Retrocopy THSHIYNWER*HDYQFSYHDWPIPNNFDIDKVQHDPRTLSDVTDEEEVQEDPQKYFDGDHEKSLQDPAFD

Parental  THFSTEPCWQYPDHHENKYCDLECSHTCNYKMRSSSYLDNLVWRESEVNHYYEPKLIIDLSNWKEQSKEK
          THFSTEPCWQY.DHHENKYCDLECSHTCNYKMRSS.YLDNLVWRESEVNHYYE.KLIIDLSNWKEQSKEK
Retrocopy THFSTEPCWQYSDHHENKYCDLECSHTCNYKMRSS*YLDNLVWRESEVNHYYELKLIIDLSNWKEQSKEK

Parental  SDKKGKSKCERNGLVKAQIALEEASQQLVEKEREKNQGFDFDSFIAGTIQLSSQHESTDVVDKLNDLNSS
          .DKKGKSKCERNGLVK.QI..EEASQQLVEKEREKNQ.F.F.SFIAGTIQLSSQHESTDVV.KLNDLNSS
Retrocopy YDKKGKSKCERNGLVKTQITPEEASQQLVEKEREKNQRFNFYSFIAGTIQLSSQHESTDVVNKLNDLNSS

Parental  VSQLELKTLISKSVSREKQEKGMANLAQLEALYQSSWESQYVSGGEECFLIDQFCCEVRKDEQIEKENTY
          V.QLELKTLISKSVSREKQEKGMANL.QLEALYQSSWESQYVSGGE.CFL..QFCCEVRKDEQI.KENTY
Retrocopy VTQLELKTLISKSVSREKQEKGMANLVQLEALYQSSWESQYVSGGEKCFLKEQFCCEVRKDEQIKKENTY

Parental  TSYLDKFFSRKEDTEMLETEPVEDGKFGERESEEGFLNNS-GEFL-FNKQLESIGIPQFHSPVGSPLKSI
          T.YLDKFFSR.EDTEMLET.PVED.KFG.RESEEGFLNN...EFL.F.KQ.ES.GI.QFHSP..SP.K..
Retrocopy TNYLDKFFSRQEDTEMLETDPVEDCKFGKRESEEGFLNNR<EEFLIFLKQFESKGISQFHSPADSPFK*L

Parental  QATLTPSAMKSSPQIPHKTYSSILKHLN
          .ATL.PSAMKSSPQIP.KT.SSILK.LN
Retrocopy *ATLIPSAMKSSPQIPPKTHSSILKYLN

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_445 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000962	1 retrocopy	retro_cjac_2633,
Homo sapiens	ENSG00000069956	2 retrocopies	retro_hsap_1257, retro_hsap_2519,
Gorilla gorilla	ENSGGOG00000004003	1 retrocopy	retro_ggor_1571,
Monodelphis domestica	ENSMODG00000001962	2 retrocopies	retro_mdom_138, retro_mdom_63,
Nomascus leucogenys	ENSNLEG00000006476	2 retrocopies	retro_nleu_1441, retro_nleu_2095,
Otolemur garnettii	ENSOGAG00000030786	1 retrocopy	retro_ogar_1827,
Pongo abelii	ENSPPYG00000006482	2 retrocopies	retro_pabe_1853, retro_pabe_3322,
Pan troglodytes	ENSPTRG00000020224	3 retrocopies	retro_ptro_1464, retro_ptro_2743, retro_ptro_3045,
Sarcophilus harrisii	ENSSHAG00000017091	1 retrocopy	retro_shar_445 ,
Sus scrofa	ENSSSCG00000004624	1 retrocopy	retro_sscr_162,
Tupaia belangeri	ENSTBEG00000007876	2 retrocopies	retro_tbel_1879, retro_tbel_2946,
Tursiops truncatus	ENSTTRG00000016253	2 retrocopies	retro_ttru_322, retro_ttru_75,