RetrogeneDB ID: retro_shar_811

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL865182.1:199172..199680(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAE1
• Ensembl ID: ENSSHAG00000002438
• Aliases: None
• Description: RAE1 RNA export 1 homolog (S. pombe) [Source:HGNC Symbol;Acc:9828]

Sequence

>retro_shar_811
CAGTATGATGCCGCTTTGAAAACTGTGCATTGGATCAAAGCACCGACTATAGTTGTGCAATGGCAGGAAGTTGGAATAAA
ATGTCAAAGTTTTGGGACACATGGTTGTCTAGTCCTGTGATGACACTGCAGCTACCTGAAAGATATTATTGTGTTGACAT
GGTCTATCCCATGACGCTATAGTTATAGTTGAGAGAGGACCAATAGTTTGTCAATTAGAAAATCAGCCTTCTGAATTCAG
GAGAATAGAATCTCCTCTTAAATATCAACATCACTGTGTTGCCATTTTTAAAGACAAACAGAAGAAGCCTACTGGTTTTG
CTCTGGGAAGTATTAAAAGAAGAGTTGCTATTTATTACATTAATCCACCAAATCCTGCCAAAGATAACTTCACCTTTAAA
TGTCATTGTTCTAAAGGAAGTAATATTTCAGCTTCTCAAGATATCTATGCTGTGAATGGGCTAGCATTTCATCCTGTTCA
TGGAACTCTTGCAATCACAGAATCTGAT

Alignment

ORF - retro_shar_811 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.16 %
• Parental protein coverage: 69.67 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KHDAPVKTVHWIKAP-NYSCVMTGSWDKTLKFWDTRSPSPMMTLQLPERCYCADVVYPMA-AVATAERGL
          ..DA..KTVHWIKAP..YSC.M.GSW.K..KFWDT...SP.MTLQLPER.YC.D.VYPM..A....ERG.
Retrocopy QYDAALKTVHWIKAP<DYSCAMAGSWNKMSKFWDTWLSSPVMTLQLPERYYCVDMVYPMT<AIVIVERGP

Parental  IVYQLENQPSEFRRIESPLKHQHRCVAIFKDKQNKPTGFALGSIEGRVAIHYINPPNPAKDNFTFKCHRS
          IV.QLENQPSEFRRIESPLK.QH.CVAIFKDKQ.KPTGFALGSI..RVAI.YINPPNPAKDNFTFKCH.S
Retrocopy IVCQLENQPSEFRRIESPLKYQHHCVAIFKDKQKKPTGFALGSIKRRVAIYYINPPNPAKDNFTFKCHCS

Parental  NGTNTSAPQDIYAVNGIAFHPVHGTLATVGSD
          .G.N.SA.QDIYAVNG.AFHPVHGTLA...SD
Retrocopy KGSNISASQDIYAVNGLAFHPVHGTLAITESD

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_811 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 6 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryctolagus cuniculus	ENSOCUG00000001585	2 retrocopies	retro_ocun_1819, retro_ocun_646,
Otolemur garnettii	ENSOGAG00000014649	2 retrocopies	retro_ogar_1400, retro_ogar_2829,
Ochotona princeps	ENSOPRG00000000228	1 retrocopy	retro_opri_1149,
Sarcophilus harrisii	ENSSHAG00000000550	1 retrocopy	retro_shar_812,
Sarcophilus harrisii	ENSSHAG00000002438	1 retrocopy	retro_shar_811 ,
Sarcophilus harrisii	ENSSHAG00000010372	1 retrocopy	retro_shar_358,