RetrogeneDB ID: retro_shar_51

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL856993.1:919840..920638(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000011855
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: BRCC3
• Ensembl ID: ENSSHAG00000005392
• Aliases: None
• Description: BRCA1/BRCA2-containing complex, subunit 3 [Source:HGNC Symbol;Acc:24185]

Sequence

>retro_shar_51
GCGGGATTCGCCATGGCCGTGGTGGCCGTGCACCTGGACTCGGACGCCTTCCTGGTGTGCCTCAACCACGCCCTGAGCAC
GGAGAAGGAGGAGGTGATGGGGCTGTGCATCGGCGAGGTGGACGCCTGCAAGATCGTGCACATCCACTCGGTGATCATCC
TGCGGCGCTCGGACAAGCGCAAGGACCGCGTGGAGATCTCCCCCGAGCAGCTGTCGGCCGCGTCCACGGAGGCCGAGCGC
CTGGCCGAGCTCACGGGCCGCCCGGTGCGCGTGGTGGGCTGGTATCACTCGCACCCGCACATCACCGTGTGGCCGTCGCA
CGTGGACGTGCGCACGCAGGCCATGTACCAGATGATGGACCAGGGCTTCGTGGGCCTCATCTTCTCCTGCTTCATCGAGG
ACAAGAACACCAAGACCGGCCGCCTCCTGTACACGTGCTTCCAGTCGGTGCAGGCGCAGAAGAGCGCCGACTACGAGCGG
ATCGAGATCCCCATCCACGTGGTGCCGCACGACACCATCGGCAAGGTGTGCCTCGAGTCGGCCATCGAGTTACCCAAGAT
CCTTTGCCAGGAGGAGCAGGACGCGTACCGGCGCATCCACAGCCTCTCCCACCTGGACTCGGTCACCATGATCCACAACG
GCTCCGTCTTCACCAAGAACCTCTGCAGCCAGATGTCGGCCATCAGCGGGCCCCTGCTGCAGTGGCTGGAGGACCGGCTG
CAGCAGAACCAGCAGCGCGCGCGGGAACTGCAGCGGGAAAAGGAGCAGCTGCTGCAGGAGCTGGCCACCCTGGATTGA

Alignment

ORF - retro_shar_51 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VEVGKIVHIHSVIVLRRSDKRKDRVEISPEQLSAASLEAEILTELTGRPMRVVGWYHSHPHITVWPSHVD
          V...KIVHIHSVI.LRRSDKRKDRVEISPEQLSAAS.EAE.L.ELTGRP.RVVGWYHSHPHITVWPSHVD
Retrocopy VDACKIVHIHSVIILRRSDKRKDRVEISPEQLSAASTEAERLAELTGRPVRVVGWYHSHPHITVWPSHVD

Parental  IRTQAMYQMMDESFVGLIFSCFIEDKNTKTGRVLYTCFQSVQAQKGSEYERVDVPLHVLPQDTMGKASLE
          .RTQAMYQMMD..FVGLIFSCFIEDKNTKTGR.LYTCFQSVQAQK...YER...P.HV.P.DT.GK..LE
Retrocopy VRTQAMYQMMDQGFVGLIFSCFIEDKNTKTGRLLYTCFQSVQAQKSADYERIEIPIHVVPHDTIGKVCLE

Parental  AAIELPKILCQEEQDAYRKIHSLTHLDAVTKIHNGSEVFTKNLCNQMSAISGPLMQWLEDRRDYNRKLLL
          .AIELPKILCQEEQDAYR.IHSL.HLD.VT.IHNGS.VFTKNLC.QMSAISGPL.QWLEDR...N.....
Retrocopy SAIELPKILCQEEQDAYRRIHSLSHLDSVTMIHNGS-VFTKNLCSQMSAISGPLLQWLEDRLQQNQQRAR

Parental  QLELEKVALQEELDSLD
          .L..EK..L..EL..LD
Retrocopy ELQREKEQLLQELATLD

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_51 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 9 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007817	2 retrocopies	retro_btau_1327, retro_btau_1646,
Cavia porcellus	ENSCPOG00000001882	2 retrocopies	retro_cpor_388, retro_cpor_627,
Homo sapiens	ENSG00000185515	1 retrocopy	retro_hsap_3271,
Gorilla gorilla	ENSGGOG00000027248	1 retrocopy	retro_ggor_2226,
Monodelphis domestica	ENSMODG00000016487	1 retrocopy	retro_mdom_930,
Mus musculus	ENSMUSG00000031201	1 retrocopy	retro_mmus_672,
Nomascus leucogenys	ENSNLEG00000014460	1 retrocopy	retro_nleu_2940,
Sarcophilus harrisii	ENSSHAG00000005392	1 retrocopy	retro_shar_51 ,
Ictidomys tridecemlineatus	ENSSTOG00000019781	2 retrocopies	retro_itri_1271, retro_itri_806,