RetrogeneDB ID: retro_shar_5

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL849703.1:3888426..3888909(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000018653
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000008480
• Aliases: None
• Description: None

Sequence

>retro_shar_5
CTGGAAAACGAACTGATGTATGGAGTTCCTTTTGAATTTCCAGAGAAGGCTCAGTCAAAAGATTTCCTGATTCCCATTGG
AAAAGCTAAAATAGAAAGGGAAGGAGCCCATATTACATTGGTTTCCCATTCACGATCTATTGGCCATTGTATGGAAGCAG
CTGCTATACTGTCTAAAGAGGGAATAGAATGTGAGGTGATCAATCTGTGCACCATTAGACTGATGGACATTGAGACCATC
GAGTTTAGTGTCATGAAGACCAATCACCTTGTGACGGTTGAAGGAGGCTGGCCCCAGTTTGGAGTAGGAGCCGAGATCTG
TGCCAGGATCATGGAAGGTCCCACCTTTAACTTCCTCAATGCTCCTGCTGTCCGAGTCACAGGGGCCAATGTTCCTATGC
CTTATGCAAAGATACTGGAAGAAAACTGCATTCCACAAGTCAAAGACATCATCTTTGCAGCCAAGAAAACTCTCAATATC
TAA

Alignment

ORF - retro_shar_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.38 %
• Parental protein coverage: 59.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LENELMYGVPFEFPEEAQSKDFLIPIGKAKIEREGTHITLVSHSRPVGHCMEAAAILSKEGIECEVINLR
          LENELMYGVPFEFPE.AQSKDFLIPIGKAKIEREG.HITLVSHSR..GHCMEAAAILSKEGIECEVINL.
Retrocopy LENELMYGVPFEFPEKAQSKDFLIPIGKAKIEREGAHITLVSHSRSIGHCMEAAAILSKEGIECEVINLC

Parental  TIRPMDIETIEFSVMKTNHLVTVEGGWPQFGVGAEICARIMEGPAFNFLDAPAVRVTGADVPMPYAKILE
          TIR.MDIETIEFSVMKTNHLVTVEGGWPQFGVGAEICARIMEGP.FNFL.APAVRVTGA.VPMPYAKILE
Retrocopy TIRLMDIETIEFSVMKTNHLVTVEGGWPQFGVGAEICARIMEGPTFNFLNAPAVRVTGANVPMPYAKILE

Parental  ENCIPQVKDIIFAAKKTLNI
          ENCIPQVKDIIFAAKKTLNI
Retrocopy ENCIPQVKDIIFAAKKTLNI

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_5 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021724	1 retrocopy	retro_btau_596,
Canis familiaris	ENSCAFG00000007340	2 retrocopies	retro_cfam_1215, retro_cfam_2031,
Callithrix jacchus	ENSCJAG00000019739	1 retrocopy	retro_cjac_3875,
Dasypus novemcinctus	ENSDNOG00000006937	1 retrocopy	retro_dnov_1090,
Monodelphis domestica	ENSMODG00000002398	1 retrocopy	retro_mdom_614,
Mus musculus	ENSMUSG00000021748	1 retrocopy	retro_mmus_290,
Oryctolagus cuniculus	ENSOCUG00000015632	1 retrocopy	retro_ocun_342,
Procavia capensis	ENSPCAG00000016595	1 retrocopy	retro_pcap_261,
Sarcophilus harrisii	ENSSHAG00000008480	1 retrocopy	retro_shar_5 ,
Ictidomys tridecemlineatus	ENSSTOG00000019553	2 retrocopies	retro_itri_1349, retro_itri_249,
Tupaia belangeri	ENSTBEG00000016148	2 retrocopies	retro_tbel_1651, retro_tbel_3170,