RetrogeneDB ID: retro_shar_21

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834625.1:2149323..2149968(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000016395
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000011544
• Aliases: None
• Description: None

Sequence

>retro_shar_21
ATGCAGCAGCCACCACGGCAGCTCGAGTTAGGGGAAGGCAATCTTCCCGTGTTCGTGTTTCCAACGGAGCTTATCTTTTA
TGCAGACGACCAGTCCACCCACAAGCAGGTGCTGACTCTGTATAATCCCTACGAGTTTGCCTTGAAGTTCAAAGTGCTGT
GCACCACCCCCAACAAGTACGTGGTTGTGGACGCCGCGGGTGCAGTGAAGCCTCAGTGCTGCGTGGACATCGTAATTCGT
CATAGAGATGTCCGGCCCTGTCACTATGATGTAATAGACAAATTCCGTCTACAAGTTTCCGAACAAAGCCAGAGGAAGGC
TTTAGGACGCAAAGAGATTATTGCGACCCTTCTGCCGTCGGCCAAGGAACAACGAAAGGAAGAAGAGGAAAAAAGGATAA
AGGAACACTTAGCAGAAAGTGTGTTTTTTGAGCAGATGCTGTCTCAAACGGAAAACAGGGCTGTTTCATCTGGACCTAGT
TTATTAACTGTCTTCCTGGGAATAGTGTGCATTGCAGCTCTTATGCTTCCCACACTGGGAGAAGTGGAATCTCTAGTGCC
TCACTACTTTCATTTAAGTGTGAATCAAAAATTAGTAGCTGCTTATGTTTTAGGTCTTATCACTATGGTCATTCTTAGAA
TATGA

Alignment

ORF - retro_shar_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.93 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MQQQRRQPELVEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVK
          MQQ..RQ.EL.EGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVK
Retrocopy MQQPPRQLELGEGNLPVFVFPTELIFYADDQSTHKQVLTLYNPYEFALKFKVLCTTPNKYVVVDAAGAVK

Parental  PQCCVDIVIRHRDVRSCHYDVIDKFRLQVSEQSQRKALGRKEIIATLLPSAKEQRKEVEEKRIKEHLTES
          PQCCVDIVIRHRDVR.CHYDVIDKFRLQVSEQSQRKALGRKEIIATLLPSAKEQRKE.EEKRIKEHL.ES
Retrocopy PQCCVDIVIRHRDVRPCHYDVIDKFRLQVSEQSQRKALGRKEIIATLLPSAKEQRKEEEEKRIKEHLAES

Parental  VFLEQMLCQTENRTASSGPSLLTVFLGIVCVAALMLPTLGEVESLVPLYFHLSVNQKLVAAYVLGLITMV
          VF.EQML.QTENR..SSGPSLLTVFLGIVC.AALMLPTLGEVESLVP.YFHLSVNQKLVAAYVLGLITMV
Retrocopy VFFEQMLSQTENRAVSSGPSLLTVFLGIVCIAALMLPTLGEVESLVPHYFHLSVNQKLVAAYVLGLITMV

Parental  ILRI
          ILRI
Retrocopy ILRI

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_21 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001304	1 retrocopy	retro_amel_683,
Choloepus hoffmanni	ENSCHOG00000007386	5 retrocopies	retro_chof_1202, retro_chof_1623, retro_chof_201, retro_chof_2295, retro_chof_675,
Dasypus novemcinctus	ENSDNOG00000013117	4 retrocopies	retro_dnov_1825, retro_dnov_2650, retro_dnov_2660, retro_dnov_926,
Macaca mulatta	ENSMMUG00000022505	1 retrocopy	retro_mmul_133,
Monodelphis domestica	ENSMODG00000015178	1 retrocopy	retro_mdom_159,
Mus musculus	ENSMUSG00000023074	1 retrocopy	retro_mmus_291,
Otolemur garnettii	ENSOGAG00000005739	2 retrocopies	retro_ogar_2508, retro_ogar_528,
Sarcophilus harrisii	ENSSHAG00000011544	1 retrocopy	retro_shar_21 ,
Sus scrofa	ENSSSCG00000012686	1 retrocopy	retro_sscr_690,
Ictidomys tridecemlineatus	ENSSTOG00000008152	1 retrocopy	retro_itri_1303,
Tarsius syrichta	ENSTSYG00000006102	1 retrocopy	retro_tsyr_1785,