RetrogeneDB ID: retro_shar_587

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL850744.1:6171..7824(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CBS
• Ensembl ID: ENSSHAG00000017100
• Aliases: None
• Description: cystathionine-beta-synthase [Source:HGNC Symbol;Acc:1550]

Sequence

>retro_shar_587
ATGCTTTGTGATCCTTCCCCAATCGAGAGGGAAACCAAGGTTTGCCCTCATCTCTCTAATAACAACCTGGAGAATGTGAA
ATTAGAGACATCATCTAATTGTGGGAACAAAGTTGAGAAAGAACGAAAGTGGATCTGGCCTGACCATCCTAGCAAGTGTA
CTTGGCAGCTAGGCAAACCTGTCTCAGAATCTCCTCATCATCAGGTCTCCTTGTCAAAGATAACCAAAGTCATTCGTAAT
ATTTTGAAGAAAATTGGAGATACACCTATGGTCAGAATCAATAAAATTGGGAAGAACTTTGGACTGAAATGTGAACTTTT
GGCAAAGTGTGAATTTTTCAATGCTGGAGGGAGTGTGAAGGATCGAATCAGCCTGAGAATGGTAGAAGATGCAGAAAGAG
CAGGCATTTTGAAACCTGGACATACAATCATCGAGCCAACTTCTGGGAATACCTGAATTGGGCTGGCCCTGGATGCAGCA
GTAAAAGGGTATCATTGAATCATTGTGATGCCAGAGAAAATGAGTATGGAAAAGGTGGTTGTCCTGAGAGCACTGGGAGC
TGAAATTATGAGAACTCCAACCAGTGCCAGATTTGATTCCCCTGAATCTCATGTAGAAGTGGCATGGCAACTGAAAAATG
AGATTCCCAATTCTCAAATTTTGGAGCAATATTGAAATGCCAATAATCTTCTCGCTCACTATGATAGCACAGCAGAGGAG
ATCTTACAGCAATGTGATGGGAAATTGGAAATATTGGTAGCTTCTGCTGGCACTGGGGGCACAATTACAGGTCTTGCCTG
AAAGCTGAAGGAGAAATGTCCAGGATGAAAAATCATTGGTGTTGATCCAGAAGGATCTATCCTTGCTGAGCCAGAAGAAC
TGAACCAGAGCTACAAAACAGTTTATGAAGTAGAGGGCATTGGGTATGATTTCATCCCCACAGTACTAGACAGGAAGATG
GTGGATAAGTGGTACAAGAGCAATGATGAAGGCTCTTTTGCTTTTGCTGGAATGTTAATTGTGCAAGAAGGATTACTTTG
TGGTGGTAGCTCTGGTAGTTCGATGTCTGTTGCAGTAAAGGCTGCCAAGGATCTGAAGGAGGGTTGTGTGGTCATTTTGC
CTGATTCTGTGAGGGATTACATGTTCAAATTTCTGAGTGACAAGTGGATGCTTCAGAAGGGATTTATGAAGGAAGAAGAT
ATGATGATTACTAAGCTATGGTGGTGGCACCTCAAGATTCAAGAATTAAGCCTCTCTTCACTTTTGACAGTCTTACCAAC
TGTCACTTGTGAACGAACTATTGAAATCCTCCGAGAGAAGGGTTGTGACCAGGTACCAGTTGTTGATGAATCTGGTTTGA
TATTGGAAATGGTCACTCTTGGTAATATGCTTTCATCCTTGCTTGCTGGGAAGGTTCAGCCTTCAGACCAAGCCAGCAAA
GTCATCTATAAGCAATTTCATCAGATTCACCTGACCGACACCTTGGGGATGCTTTCCCACATCCTGGAGACAAAACATTT
TGCTCTAGTGGTTCACAAACAGATTCAGTATCACAGCAATGGCAACTCCAATCAAAGACATATGGTGTTTGGTGTTGTCA
CAGCTATTGATCTGCTGAATTTTGTGGCTGCCCAAGAAAGAGAACAGAAGACA

Alignment

ORF - retro_shar_587 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRDPSPVERETKVCPHLSSNNLENVNLETSANCGNKVEKERKWIRPDNPSKCTWQLGKPISESPHHHVS
          ML.DPSP.ERETKVCPHLS.NNLENV.LETS.NCGNKVEKERKWI.PD.PSKCTWQLGKP.SESPHH.VS
Retrocopy MLCDPSPIERETKVCPHLSNNNLENVKLETSSNCGNKVEKERKWIWPDHPSKCTWQLGKPVSESPHHQVS

Parental  LSKTTKVIPNILKKIGDTPMVRINKIGKNFGLKCELLAKCEFFNAGGSVKDRISLRMVEDAERAGILKPG
          LSK.TKVI.NILKKIGDTPMVRINKIGKNFGLKCELLAKCEFFNAGGSVKDRISLRMVEDAERAGILKPG
Retrocopy LSKITKVIRNILKKIGDTPMVRINKIGKNFGLKCELLAKCEFFNAGGSVKDRISLRMVEDAERAGILKPG

Parental  HTIIEPTSGNTGIGLALAAAVKGYRCIIVMPEKMSMEKVDVLRALGAEIVRTPTSARFDSPESHVGVAWR
          HTIIEPTSGNT.IGLAL.AAVKGY..IIVMPEKMSMEKV.VLRALGAEI.RTPTSARFDSPESHV.VAW.
Retrocopy HTIIEPTSGNT*IGLALDAAVKGYH*IIVMPEKMSMEKVVVLRALGAEIMRTPTSARFDSPESHVEVAWQ

Parental  LKNEIPNSHILDQYRNACNPLAHYDGTAEEILQQCDATGKLDMLVASAGTGGTITGLARKLKEKCPECKI
          LKNEIPNS.IL.QY.NA.N.LAHYD.TAEEILQQCD..GKL..LVASAGTGGTITGLA.KLKEKCP..KI
Retrocopy LKNEIPNSQILEQY*NANNLLAHYDSTAEEILQQCD--GKLEILVASAGTGGTITGLA*KLKEKCPG*KI

Parental  IGVDPEGSILAEPEELNQSDKTAYEVEGIGYDFIPTVLDRKVVDKWYKSNDEDSFAFARMLIAQEGLLCG
          IGVDPEGSILAEPEELNQS.KT.YEVEGIGYDFIPTVLDRK.VDKWYKSNDE.SFAFA.MLI.QEGLLCG
Retrocopy IGVDPEGSILAEPEELNQSYKTVYEVEGIGYDFIPTVLDRKMVDKWYKSNDEGSFAFAGMLIVQEGLLCG

Parental  GSSGSSMSIAVKAAKDLKEGQRCVVILPDSVRNYMSKFLSNKWMLQKGFMKEEEMMITKPWWWHLKIQEL
          GSSGSSMS.AVKAAKDLKEG..CVVILPDSVR.YM.KFLS.KWMLQKGFMKEE.MMITK.WWWHLKIQEL
Retrocopy GSSGSSMSVAVKAAKDLKEG--CVVILPDSVRDYMFKFLSDKWMLQKGFMKEEDMMITKLWWWHLKIQEL

Parental  SLSAPLTVLPTVTCERTIEILREKGFDQVPVVDESGLILGMVTLGNMLSSLLAGKVQPSDQVSKVIYKQF
          SLS..LTVLPTVTCERTIEILREKG.DQVPVVDESGLIL.MVTLGNMLSSLLAGKVQPSDQ.SKVIYKQF
Retrocopy SLSSLLTVLPTVTCERTIEILREKGCDQVPVVDESGLILEMVTLGNMLSSLLAGKVQPSDQASKVIYKQF

Parental  RQIHLTDTLGMLSHILETDHFALVVHEQIQYHSNGSSNQRHMVFGIVTAIDLLNFVAAREREQKT
          .QIHLTDTLGMLSHILET.HFALVVH.QIQYHSNG.SNQRHMVFG.VTAIDLLNFVAA.EREQKT
Retrocopy HQIHLTDTLGMLSHILETKHFALVVHKQIQYHSNGNSNQRHMVFGVVTAIDLLNFVAAQEREQKT

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_587 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000009950	1 retrocopy	retro_lafr_383,
Oryzias latipes	ENSORLG00000008831	1 retrocopy	retro_olat_55,
Sarcophilus harrisii	ENSSHAG00000017100	1 retrocopy	retro_shar_587 ,