RetrogeneDB ID: retro_shar_74

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834728.1:995265..996018(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000012254
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000018132
• Aliases: None
• Description: None

Sequence

>retro_shar_74
ATGAATGGAAGGACTGATTTTGGAACAGAACAGAATGCAGAAGTCTCACCACCACTCCCCAACATTGGAATGGATTACAT
ACCAACAGAAGAAGAAAGAAAAGTCTTTGCTGAATGTAATCGAGAGAGCTTCTGGTACAGATCTGTTCCCTTTTCTGCAA
CTAGTGTGTTGGTTACTCAGGGATTAATTACTAAAGGAATTCTTTCCAGTCATCCCAAATATGGTTCTATCCCTAAAATT
GCATTTGCTTGCATAATGGGATATTTTGCTGGAAAAATTTCCTATGTGAAAACTTGCCAAGAGAAGTTTAAACGACTTGA
AAATTCTCCTCTTGGAGAAGTTCTGCAAATGGGACCAGCACGTCGATTTGCATCACCTGGGTATTTTTCACAAAAGTCAG
AATTTGATTCAAAAATGCCTCCACAGTCATCTTTTGGAACATCTCCAACTTCTGAAAGCAGTGCAAAAGAAAGTGCTTTT
CCTCCTTATGAACCAGTCCCCTTCAGTGCTTCCATGAATGAATCCTCTCCTACTGGTATTACTGATTATAATGCCCAAGG
ACCTGATACAATTGTGGAAGAAAGTCCTAAGAGAAAAGTTGTTACATATGAAGAATTAAGGAATAAGAACAGAGAAACAT
ATGAAGTAACCTTGTCACAAAAAGGTGATACCCCACTTCGGTCTGTGCAAAAAAGAGCACCAAAAAAAAAACAAGGGAAA
GTAAACCAATATGGAGATACTTGGGATGAGTGA

Alignment

ORF - retro_shar_74 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.8 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNGRTDFGTEQNAEVSPPLPNIGMDYIPTEEERKVFAECNRESFWYRSVPFSATSVLVTQGLITKGILSS
          MNGRTDFGTEQNAEVSPPLPNIGMDYIPTEEERKVFAECNRESFWYRSVPFSATSVLVTQGLITKGILSS
Retrocopy MNGRTDFGTEQNAEVSPPLPNIGMDYIPTEEERKVFAECNRESFWYRSVPFSATSVLVTQGLITKGILSS

Parental  HPKYGSIPKIAFACIMGYFAGKISYVKTCQEKFKRLENSPLGEVLRMGPARRFASPGYFSQKSEFDSKMP
          HPKYGSIPKIAFACIMGYFAGKISYVKTCQEKFKRLENSPLGEVL.MGPARRFASPGYFSQKSEFDSKMP
Retrocopy HPKYGSIPKIAFACIMGYFAGKISYVKTCQEKFKRLENSPLGEVLQMGPARRFASPGYFSQKSEFDSKMP

Parental  PQSSFGTSPTSESSAKESAFPPYEPVPFSASMNESSPTGITDYNAQGPDTIVEESPKRKVVTYEELRNKN
          PQSSFGTSPTSESSAKESAFPPYEPVPFSASMNESSPTGITDYNAQGPDTIVEESPKRKVVTYEELRNKN
Retrocopy PQSSFGTSPTSESSAKESAFPPYEPVPFSASMNESSPTGITDYNAQGPDTIVEESPKRKVVTYEELRNKN

Parental  RETYEVTLSQKGDTPLRSVQERAP-KKQGKVNQYGDTWDE
          RETYEVTLSQKGDTPLRSVQ.RAP.KKQGKVNQYGDTWDE
Retrocopy RETYEVTLSQKGDTPLRSVQKRAPKKKQGKVNQYGDTWDE

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_74 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000011863	1 retrocopy	retro_cpor_928,
Echinops telfairi	ENSETEG00000005961	1 retrocopy	retro_etel_1731,
Latimeria chalumnae	ENSLACG00000014002	1 retrocopy	retro_lcha_88,
Macropus eugenii	ENSMEUG00000010655	2 retrocopies	retro_meug_1692, retro_meug_2016,
Monodelphis domestica	ENSMODG00000020640	1 retrocopy	retro_mdom_1103,
Sarcophilus harrisii	ENSSHAG00000018132	1 retrocopy	retro_shar_74 ,
Ictidomys tridecemlineatus	ENSSTOG00000014963	1 retrocopy	retro_itri_986,