RetrogeneDB ID: retro_shar_82

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL835748.1:55831..56182(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000003218
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000007434
• Aliases: None
• Description: None

Sequence

>retro_shar_82
ATGAAATTCCAATACAAGGAAGATCATCCTTTCCAGTACTGGAAAAAAGAAGGGGAGAAGATTCGGAAGAAATACCCTGA
CAGAGTCCCTGTGATTGTGGAGAAGGCACCTACAGCCAGAGTCCCTGACCTGGATAAAAGGAAGTACCTGGTACCCTCTG
ACCTAACAGTTGGTCACTTCTACTTCTTAATTGGGAAACGGATCCATCTTCGGCCAGAAAGCGCCCTATTCGTCTTCGTT
AACAACCCTATCCCTCCTACTAGTGCTATTGTGGACCAACTTTATGAGGACAACCATGAGGAAGACTGTTTTCTCTATGT
TGCCTACAGTGATGATAGCCTCCATGGGAAG

Alignment

ORF - retro_shar_82 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.18 %
• Parental protein coverage: 86.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFQYKEDHPFEYRKKEGEKIRKKYPDRVPVIVEKAPKARVPDLDKRKYLVPSDLTVGQFYFLIRKRIHL
          MKFQYKEDHPF.Y.KKEGEKIRKKYPDRVPVIVEKAP.ARVPDLDKRKYLVPSDLTVG.FYFLI.KRIHL
Retrocopy MKFQYKEDHPFQYWKKEGEKIRKKYPDRVPVIVEKAPTARVPDLDKRKYLVPSDLTVGHFYFLIGKRIHL

Parental  RPEDALFFFVNNTIPPTSATMGQLYEDNHEEDYFLYVAYSDESVYGK
          RPE.ALF.FVNN.IPPTSA...QLYEDNHEED.FLYVAYSD.S..GK
Retrocopy RPESALFVFVNNPIPPTSAIVDQLYEDNHEEDCFLYVAYSDDSLHGK

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_82 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.

---

Parental genes homology:

Parental genes homology involve 13 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001218	1 retrocopy	retro_chof_329,
Cavia porcellus	ENSCPOG00000006718	1 retrocopy	retro_cpor_232,
Equus caballus	ENSECAG00000014832	1 retrocopy	retro_ecab_673,
Homo sapiens	ENSG00000139112	1 retrocopy	retro_hsap_60,
Gorilla gorilla	ENSGGOG00000022360	1 retrocopy	retro_ggor_1219,
Macropus eugenii	ENSMEUG00000002873	3 retrocopies	retro_meug_1584, retro_meug_1840, retro_meug_905,
Macaca mulatta	ENSMMUG00000002197	1 retrocopy	retro_mmul_2235,
Oryctolagus cuniculus	ENSOCUG00000016834	3 retrocopies	retro_ocun_1380, retro_ocun_496, retro_ocun_697,
Sarcophilus harrisii	ENSSHAG00000007434	1 retrocopy	retro_shar_82 ,
Sarcophilus harrisii	ENSSHAG00000017074	1 retrocopy	retro_shar_168,
Ictidomys tridecemlineatus	ENSSTOG00000002246	1 retrocopy	retro_itri_391,
Tarsius syrichta	ENSTSYG00000005307	19 retrocopies	retro_tsyr_1045, retro_tsyr_1070, retro_tsyr_1101, retro_tsyr_1137, retro_tsyr_1308, retro_tsyr_1413, retro_tsyr_1467, retro_tsyr_1481, retro_tsyr_1671, retro_tsyr_1765, retro_tsyr_1800, retro_tsyr_234, retro_tsyr_573, retro_tsyr_761, retro_tsyr_796, retro_tsyr_832, retro_tsyr_864, retro_tsyr_978, retro_tsyr_999,
Tursiops truncatus	ENSTTRG00000009099	3 retrocopies	retro_ttru_1451, retro_ttru_1563, retro_ttru_1629,