RetrogeneDB ID: retro_shar_15

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864882.1:1862961..1863711(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000015630
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000007152
• Aliases: None
• Description: None

Sequence

>retro_shar_15
ATGGCGTCAGGAGTGGAGACTGAGACTCGCCCAGAGACCCTGGAGTATGAGGAGGAGGAAAAGGAACGACCCCTGACTGC
GGCCGAGGCGCTGGCTGCCCAGAAACGAGAAGAGAGACTGAGGAAGTTTCGGGAGCTGCACATGAAAAGAAATGAGGCCC
GAAAATTAAATCATCAGGAGGTTGTGGAGGAAGATAAAAGGCTCAAGCTGCCAGCCAACTGGGAGGCTAAGAAGGCTCGT
TTGGAATGGGAGCTACAGGTTGAAGAAAAGAAGAAGGAATGTGCTGCAAGGGGAGAAGATTATGAACGAGTGAAATTACT
GGAGATCAGTGCTGAAGATGCAGCAAGATGGAAGAGAAAGAAGAAGAGGAAGAACCCAGATTTGGGCTTTTCAGACTATG
CAGCTGCTCAGTTACGCCAATATCACCGATTAACCAAGCAGATCAAACCAGATATGGAAGCATATGAAAAACTGAGAGAA
AAATATGGAGAAGAATTCTACCCAACATCCAATAGTCTTCTTCATGGAACACATGTACCTTCTACAGAAGAAATTGATAG
GATGGTTGTAGATCTAGACAAACAAATTGAGAAACGAGAAAAATACAGCCGGAGACGTCCTTATAATGATGACTCTGATA
TTGACTACATCAATGAAAGAAATGCCAAATTCAACAAAAAAGCCGAGAGATTCTATGGAAAGTATACAGCTGAAATCAAA
CAGAATTTGGAAAGAGGAACAGCTGTTTAA

Alignment

ORF - retro_shar_15 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 97.09 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ELSFKRNNEARKLNHQEVVEEDKRLKLPANWEAKKARLEWELQVEEKKKECAARGEDYERVKLLEISAED
          EL..KRN.EARKLNHQEVVEEDKRLKLPANWEAKKARLEWELQVEEKKKECAARGEDYERVKLLEISAED
Retrocopy ELHMKRN-EARKLNHQEVVEEDKRLKLPANWEAKKARLEWELQVEEKKKECAARGEDYERVKLLEISAED

Parental  AERWERKKKRKNPDLGFSDYAAAQLRQYHRLTKQIKPDMEAYEKLREKYGEEFYPTSNSLLHGTHVPSTE
          A.RW.RKKKRKNPDLGFSDYAAAQLRQYHRLTKQIKPDMEAYEKLREKYGEEFYPTSNSLLHGTHVPSTE
Retrocopy AARWKRKKKRKNPDLGFSDYAAAQLRQYHRLTKQIKPDMEAYEKLREKYGEEFYPTSNSLLHGTHVPSTE

Parental  EIDRMVIDLDKQIEKREKYSRRRPYNDDSDIDYINERNAKFNKKAERFYGKYTAEIKQNLERGTAV
          EIDRMV.DLDKQIEKREKYSRRRPYNDDSDIDYINERNAKFNKKAERFYGKYTAEIKQNLERGTAV
Retrocopy EIDRMVVDLDKQIEKREKYSRRRPYNDDSDIDYINERNAKFNKKAERFYGKYTAEIKQNLERGTAV

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_15 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010115	1 retrocopy	retro_amel_566,
Bos taurus	ENSBTAG00000001651	1 retrocopy	retro_btau_478,
Choloepus hoffmanni	ENSCHOG00000005273	1 retrocopy	retro_chof_2034,
Callithrix jacchus	ENSCJAG00000018559	1 retrocopy	retro_cjac_467,
Homo sapiens	ENSG00000117614	1 retrocopy	retro_hsap_4152,
Monodelphis domestica	ENSMODG00000013951	1 retrocopy	retro_mdom_899,
Oryctolagus cuniculus	ENSOCUG00000013050	1 retrocopy	retro_ocun_1522,
Sarcophilus harrisii	ENSSHAG00000007152	1 retrocopy	retro_shar_15 ,