RetrogeneDB ID: retro_shar_296

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841251.1:295952..296202(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000006433
• Aliases: None
• Description: None

Sequence

>retro_shar_296
ATGAACTTCTTACAATTACTCATGAAGAAAAAAGAACTTATTCCTTTGGTCACATTTGTGAGTATTACTGGAATTTGAGC
AGCTTCTATGTCCATATACTCCTTTTTTCAAAAGTGATGTGATTGTTAACAGAAGAAAAAATCCAGAACCATGGGAAAAT
GTGAATCCTTACAAGCCTCAAAAGCTTCTCACAATAAACCAAAAGTGGGAACTTGTTGAAGAACTGTAGACTGTCAAAGA
ATTGACCAAA

Alignment

ORF - retro_shar_296 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MNFFQFLMKKKELIPLIAFVSIAGSGAAYMATYS-FFKSDVIVNRWQNPEPWENVNPSKPQKLVTINQRW
          MNF.Q.LMKKKELIPL..FVSI.G..AA.M..YS.FFKSDVIVNR..NPEPWENVNP.KPQKL.TINQ.W
Retrocopy MNFLQLLMKKKELIPLVTFVSITGI*AASMSIYS>FFKSDVIVNRRKNPEPWENVNPYKPQKLLTINQKW

Parental  EPVEELQAIKKLTK
          E.VEEL...K.LTK
Retrocopy ELVEEL*TVKELTK

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_296 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000031501	2 retrocopies	retro_cfam_1654, retro_cfam_669,
Cavia porcellus	ENSCPOG00000020706	1 retrocopy	retro_cpor_450,
Erinaceus europaeus	ENSEEUG00000003556	1 retrocopy	retro_eeur_594,
Monodelphis domestica	ENSMODG00000028279	1 retrocopy	retro_mdom_225,
Oryctolagus cuniculus	ENSOCUG00000029216	1 retrocopy	retro_ocun_33,
Rattus norvegicus	ENSRNOG00000050251	1 retrocopy	retro_rnor_484,
Sarcophilus harrisii	ENSSHAG00000006433	3 retrocopies	retro_shar_296 , retro_shar_416, retro_shar_744,
Ictidomys tridecemlineatus	ENSSTOG00000021929	1 retrocopy	retro_itri_1133,