RetrogeneDB ID: retro_shar_2

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834799.1:212888..213737(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000006218
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000016412
• Aliases: None
• Description: None

Sequence

>retro_shar_2
ATGAACCCACTGACCAAGGTGAAGCTTATCAATGAATTGAACGAGCGGGAGGTGGAACTCGGGGTGGCCGAAAAGGTATC
CTGGCACGCCGAATACAAGGACAGCGCTTGGATCTTTCTGGGAGGACTCCCCTATGAACTGACTGAAGGAGATATCATTT
GTGTGTTTTCTCAATACGGCGAAATTGTAAATATTAATCTTGTACGAGATAAGAAGACCGGAAAGTCCAAAGGATTCTGT
TTCCTTTGTTACGAAGATCAGAGAAGCACGATTTTGGCCGTCGACAATTTTAACGGGATCAAGATTAGAGGAAGAACTAT
CCGAGTGGATCATGTAGCTAATTACAGGCCTCCCAAGGATTCCAAGAATCTGGATAATGTAACCAGAGCACTCCGGGAAA
AGGGCTGCGGGGTTAAGACCCCGTCTCCTAGTTCGTCGGAATCCTCAGAAGATGAAACACCTGTGAAAAAGCATAAAAAA
GAGGAAAAAAGGAAGAAAAAAGACAAGGATACCAGAACAAACATGGATAAGCAGGAAACGCCCACAACATCGTCCGTAGG
GTCCCGCCACAAGACCAGGAAGGAGGAGGAGAGTTCTGGTCTGGCTAAGTCTGCCACTAGAAGCCTGGACAAGCACTCCA
GCCCTGAGCGGCGAGAAAGACGCAGACACTCAAGCGGCTCACCTGGGCTCCACCGAAGTCACCTTGAGAGAGCCGAATCT
ACCTCGAGGAGGGATTCGAGAAGGGATAAGCCGGGGCATACGAAATCCTCAAGCAGCTCCAGCAGGAAGGAAAGGAGGAG
GAAGGAAAAGCGCAAACACCGGGAAAGAAGCCACAGCTCGGACAAGCGC

Alignment

ORF - retro_shar_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.71 %
• Parental protein coverage: 84.59 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  NLFFLINRYGEIVNINLVRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIRGRTIRVDHVANYRPPKD
          ........YGEIVNINLVRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIRGRTIRVDHVANYRPPKD
Retrocopy DIICVFSQYGEIVNINLVRDKKTGKSKGFCFLCYEDQRSTILAVDNFNGIKIRGRTIRVDHVANYRPPKD

Parental  SKNLDDVTRALREKGCGVKTPSPSSSESSEDETPVKKHKKDKKEKKRKKKDKDIRTNMDKQEMPTSSSVV
          SKNLD.VTRALREKGCGVKTPSPSSSESSEDETPVKKHKK...E.KRKKKDKD.RTNMDKQE.PT.SSV.
Retrocopy SKNLDNVTRALREKGCGVKTPSPSSSESSEDETPVKKHKK---EEKRKKKDKDTRTNMDKQETPTTSSVG

Parental  SRHKTRKEKESSGLGKSATGSLDKNSSPERREGRRHLSGSPVLHRSHLERAESTSRRDSRRDKPWHKKSS
          SRHKTRKE.ESSGL.KSAT.SLDK.SSPERRE.RRH.SGSP.LHRSHLERAESTSRRDSRRDKP.H.KSS
Retrocopy SRHKTRKEEESSGLAKSATRSLDKHSSPERRERRRHSSGSPGLHRSHLERAESTSRRDSRRDKPGHTKSS

Parental  SSSSRKERRRKEKSKHRERSRSSEKR
          SSSSRKERRRKEK.KHRERS.SS.KR
Retrocopy SSSSRKERRRKEKRKHRERSHSSDKR

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_2 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002436	2 retrocopies	retro_cjac_3040, retro_cjac_4128,
Equus caballus	ENSECAG00000008257	1 retrocopy	retro_ecab_664,
Echinops telfairi	ENSETEG00000001763	1 retrocopy	retro_etel_1004,
Microcebus murinus	ENSMICG00000015139	1 retrocopy	retro_mmur_590,
Myotis lucifugus	ENSMLUG00000017095	1 retrocopy	retro_mluc_310,
Oryctolagus cuniculus	ENSOCUG00000011809	1 retrocopy	retro_ocun_106,
Pteropus vampyrus	ENSPVAG00000004425	1 retrocopy	retro_pvam_1404,
Sarcophilus harrisii	ENSSHAG00000016412	1 retrocopy	retro_shar_2 ,
Tursiops truncatus	ENSTTRG00000016210	1 retrocopy	retro_ttru_1561,