RetrogeneDB ID: retro_shar_56

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867153.1:760..1519(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000000389
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000006597
• Aliases: None
• Description: None

Sequence

>retro_shar_56
ATGACAGGTACCAGGAACCCGCTGTTGGACGGAAAGGAGTACTGCCTGACGCTGGGGGAGAGCTTCCAGAAGAGGCCCAA
GTCCTCCTTCCACACTATCCGCTATGATTTCAAACCGGCATCCATAGACACGTTGGGCGAAGGCGAGCTCCAGGTGGGCA
AAGGGGACGAGGTCACCATCACGCTGCCGAACATCCCCGGATCTGCAGCTCCAGTGAGTGTTTTCAAAGGAAACAAAAGA
CCCTATCAGAGGGACTATATTCTCATCATTAATCATGACACCGGCGAATGTGTGTTAGAAAAACTCAGTAGCAACATTCA
GGTCAAGAACATCAGAACTGAGGGATGGAGCAAAATCCGGGCGCGAATAGACCAGCCCCTGGCGCGGGCACCACCGAGGC
GCACATCAATGGGAACCCTAGTGAAGACACTGGTGGCACCAAAAACCTTCCCTGTGAAAAATACTCCTTCCTCTGAACTC
CCATTGAGTGACAATAAGCGAGAGCTGAGAGCCGAGATGGAGACCATGCAGCAGACCGGGCACCTCAGTGACAGCAGCTC
CTGTGGCTCCGAGAGCTCCAGAGGCGAAGAGGAAGAACCTGCCAACGGAACCGGGTCCTCCCGGACTCCTCCGCAGCAGT
TCAGTGGCAGAGAGCCCGTGGCCAATGGCACCACACAGCGTCCCTGGACCCCCCGGCGCTTGAACACGTTGCTAAATGAT
TTACAACTAAGCGAGTCTGGCAGTGACAGCGATGACTAG

Alignment

ORF - retro_shar_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.25 %
• Parental protein coverage: 70.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GSTPPMTVFKGNKRPYQKDCVLIINHDTGEYVLEKLSSSIQVKKTRAEGSSKIQARMEQPPARAPPPPMP
          GS..P..VFKGNKRPYQ.D..LIINHDTGE.VLEKLSS.IQVK..R.EG.SKI.AR..QP.ARAPP....
Retrocopy GSAAPVSVFKGNKRPYQRDYILIINHDTGECVLEKLSSNIQVKNIRTEGWSKIRARIDQPLARAPPRRTS

Parental  FRAPMKPPIGPKTSPVKDNPSPEPQLDDIKRELRAEVEIIEQMSSSSGSSSSDSESSSGSDDDDSSSS
          .....K....PKT.PVK..PS.E..L.D.KRELRAE.E...Q....S.SSS..SESS.G.........
Retrocopy MGTLVKTLVAPKTFPVKNTPSSELPLSDNKRELRAEMETMQQTGHLSDSSSCGSESSRGEEEEPANGT

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_56 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000006017	1 retrocopy	retro_cfam_1658,
Choloepus hoffmanni	ENSCHOG00000007449	4 retrocopies	retro_chof_1039, retro_chof_2342, retro_chof_355, retro_chof_883,
Erinaceus europaeus	ENSEEUG00000002084	1 retrocopy	retro_eeur_254,
Monodelphis domestica	ENSMODG00000014543	1 retrocopy	retro_mdom_290,
Otolemur garnettii	ENSOGAG00000013964	1 retrocopy	retro_ogar_2142,
Sorex araneus	ENSSARG00000014007	1 retrocopy	retro_sara_239,
Sarcophilus harrisii	ENSSHAG00000006597	2 retrocopies	retro_shar_485, retro_shar_56 ,