RetrogeneDB ID: retro_shar_39

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834506.1:1050711..1051761(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000012534
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011900
• Aliases: None
• Description: None

Sequence

>retro_shar_39
ATGGCAGAGGGGAAAGAGGCGACAGCGCAGGCGCAGTGCGCGACAGAGGGGGCTCGGCAACTCGGCCAAATCTTGAAAAT
CACAAGATCCATCTTCAGACTCCTAAAGATGGAGAATAAAAGGCGCCTTGCTTATTCCATCATCCAGTATCTGCATGACC
AGCTGCAGCATGGAGATCTCTCTCCTGATGCGCAGGAGAGTTTGGATGCTTCGATCCAGTGCCTGGAGACAGCTTTTGAG
GTGACTGTTGAAGACAAGTATCTGGCGGTATCCCAGACTCTGCCAGAAATGTTTGAAGCTGTTACGGGCATAAAAGAGAT
CCCCTCCGTCCATGGGAATTCTAAGCCCATCCCCCACCGTGATGTAACTACAACTGAAGCTGAGAGGCTCAAGACTGAAG
GAAATGAACAGATGAAAATGGAAAACTTTGAAGCGGCGGTGTCTTTCTATGGGAAAGCAATTGAATTAAATCCAGCCAAT
GCAGTGTATTTTTGCAACAGGGCTGCCGCCTACAGCAAACTTGGAAATTATGCAGGCGCGGTGGAAGACTGTGAAAAAGC
CATCGGCATCAACCCTTACTACAGCAAAGCCTACGGCAGAATGGCTTTAGCTCTCTCAAGTTTAAAGAAGTACAAGGAGG
CTGTAGGCTATTATAAAAAGGCTCTGAAGTTGGACCCAGACAATGACACGTACAAAACAAACCTCAAGGTAGCTGAGCAG
AAAATGAAAGAAGTCCCTAGTGCTCCAGGAGGCACTGTAGGCTGTAACCTAGCGGGCTTGCTGAACAACTCAAGCTTCAG
GAGTGTGGCGTCGAACCTCATGAATAATCCTCAAATAAGACAGATCATGTCCGGGATCATGTCAAGTGGCCACAGTACTT
TGGGAGGTTCCAGAGCCACCCGTTCTCCAAATGCCAGCCCCAGTTTCATCCAGAGAGGCCAACAGTTTGCTCAGCAGATG
CAGCAACAAAATCCAGACTTGATAGAAGAGCTCAGAAGCCAGATTAGGAATCGGAACCCCAGCACCAGCAAAGATAAAAA
GCAGGAATGA

Alignment

ORF - retro_shar_39 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.6 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEDKKRLAYSIIQFLHDQLHHGGLSPDAQESLEVAIQCLETAFGVTVEDRDLAVSKTLPEIFEAATGKKD
          ME.K.RLAYSIIQ.LHDQL.HG.LSPDAQESL...IQCLETAF.VTVED..LAVS.TLPE.FEA.TG.K.
Retrocopy MENKRRLAYSIIQYLHDQLQHGDLSPDAQESLDASIQCLETAFEVTVEDKYLAVSQTLPEMFEAVTGIKE

Parental  MSYIRRNSQPITLSDEDTAEAERLKTEGNEQMKIENFEAAVSFYGKAIELNPANAVYFCNRAAAYSKLGN
          ......NS.PI...D..T.EAERLKTEGNEQMK.ENFEAAVSFYGKAIELNPANAVYFCNRAAAYSKLGN
Retrocopy IPSVHGNSKPIPHRDVTTTEAERLKTEGNEQMKMENFEAAVSFYGKAIELNPANAVYFCNRAAAYSKLGN

Parental  YAGAVRDCERAIGIDPYYSKAYGRMGLALSSLNKHTEAVVYYKKALELDPENDTYKSNLKIAEQKMKETP
          YAGAV.DCE.AIGI.PYYSKAYGRM.LALSSL.K..EAV.YYKKAL.LDP.NDTYK.NLK.AEQKMKE.P
Retrocopy YAGAVEDCEKAIGINPYYSKAYGRMALALSSLKKYKEAVGYYKKALKLDPDNDTYKTNLKVAEQKMKEVP

Parental  SPTGGTGGFDQLAGLLNNPGFMSMASNLMNNPQVQQLMSGMISGGHNPLGAAGANPSSPNDLTSLIQAGQ
          S..GGT.G...LAGLLNN..F.S.ASNLMNNPQ..Q.MSG..S.GH..LG...A...SPN...S.IQ.GQ
Retrocopy SAPGGTVGCN-LAGLLNNSSFRSVASNLMNNPQIRQIMSGIMSSGHSTLGGSRAT-RSPNASPSFIQRGQ

Parental  QFAQQMQQQNPELIEQLRSQIRSRTPSASNDDQQE
          QFAQQMQQQNP.LIE.LRSQIR.R.PS.S.D..QE
Retrocopy QFAQQMQQQNPDLIEELRSQIRNRNPSTSKDKKQE

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_39 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005257	1 retrocopy	retro_amel_1169,
Equus caballus	ENSECAG00000010381	2 retrocopies	retro_ecab_723, retro_ecab_780,
Monodelphis domestica	ENSMODG00000004900	1 retrocopy	retro_mdom_277,
Mus musculus	ENSMUSG00000004937	1 retrocopy	retro_mmus_621,
Sarcophilus harrisii	ENSSHAG00000011900	1 retrocopy	retro_shar_39 ,