RetrogeneDB ID: retro_shar_53

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL841445.1:872182..874036(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSHAG00000011574
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSHAG00000014005
• Aliases: None
• Description: None

Sequence

>retro_shar_53
ATGGACAAGCTGGAAACAGAGAGGAAGAGCCCTGGAGAGGAGGAATATGACACAGCCGGGAGCCTGTCAGAGGAAGAGGA
CTATGTGCCTTATGTGCCTGTAAAGAAGAGAAAGCAGCAAAAGCTACAGACGTTGCTGCAGAAGCGATGGAGGGGAGAGG
CTGAGGAACAGCAGAAAGACAGTGGCAGTGAGTCCCGAGGAGATGAAGGTGACATTCCCCTGGGCCCCCAGTCCAGGGTC
AGCCTTCTGGACCAGCATCAGCTCCTGAAGGAGAAGGCAAATGCCCGCAAAGAGTCCGCTAAGGAGAAACAGCTGAAAGA
GGAAGAGAAGATCTTGGAGAGTGTGGCAGAAGGACGAGCTCTCATGTCAGTGAAGGAGATGGCCAGAGGAATCACCTACA
AGGATCCCATCAAGACCAGCTGGAAGGCCCCTCGGTATGTGCTGAGCATGTCCGCAGCCAGGCATGAGCGTGTCCGCAAG
AAGTACCAGATCTTGGTGGAAGGAGAGGGGATACCACCCCCCCTCAAAAGATTCAAGGAAATGAAGTTTCCTGCAGCCAT
TCTGAGGGGCCTGAAGAAGAAGGGAATTCACCACCCCACTCCCATCCAGATCCAGGGCATCCCTGCCGTCCTCTCTGGCC
GCGACATGATCGGCATCGCTTTCACTGGCTCTGGCAAGACATTAGTGTTCACTCTGCCCCTAATCATGTTTTGCCTGGAA
CAGGAGACAAGATTACCATTCTCCAAGAGGGAGGGGCCCTATGGGCTCATTATCTGCCCTTCTCGAGAACTGGCCCGCCA
GACCCATGGCATCTTGGACTATTACTGTCAGCTGCTGCAGGAAGACAACTACCCCTCCTTGCGCTGTGCCCTCTGCATTG
GGGGCACGTCAGTCAGGGAACAGATGGAAACTATCCGTCATGGGGTGCACGTGGTGGTGGCCACCCCTGGGCGTCTCATG
GACCTCCTACAGAAGAAAATGGTGAATCTGGACGTTTGCCGCTACCTGGCCCTGGACGAAGCTGACCGAATGATTGACAT
GGGCTTTGAGGGAGACATCAGAACCATCTTCTCCTACTTCAAGGGCCAGAGACAGACGCTGCTCTTCAGTGCTACCATGC
CCCAAAAGATCCAAAACTTTGCTAAGAGTGCTCTGGTAAAGCCTGTCATCGTCAATGTGGGCCGGGCAGGGGCTGCCAGT
CTGGATGTCATCCAGGAAGTGGAATACGTGAAGGAAGAGGTCAAGATGGTGTACCTGCTAGAGTGTCTGCAAAAGACACC
CCCACCAGTGCTGATTTTTGCAGAGAAGAAGGCGGATGTGGATGCCATCCATGAATACTTGCTTCTCAAAGGTGTGGAGG
CTGTAGCCATCCATGGGGGCAGAGATCAAGCAGAACGGAGCAAAGCCATCGAGACGTTCCGCGATGGCAAGAAAGATGTC
TTAGTGGCCACTGATGTGGCCTCCAAAGGCCTGGACTTCAGAGACATTCAGCACGTCATCAACTACGATATGCCTGTGGA
GATCGAGAATTACGTTCATCGGATTGGCCGGACAGGACGCTCTGGGAACACGGGCATGGCCACCACCTTTATCAACAAGG
CCTGTGATGAGTCAGTACTCTTGGATCTCAAAGCCCTCCTCCTTGAAGCCAAGCAGAAGGTGCCTCACATGCTGCAGGTC
CTGCACCGAGGAGATGAGTCCATGCTGGACATTGGAGGAGAGAGAGGCTGCACCTTCTGTGGGGGGCTGGGCCATCGCAT
CACTAACTGTCCCAAGCTGGAGGCCATGAAGACCAAAGAAGTCAGCAACATTGGCCGGAAGGACTACCTGGCCCATGGCT
CCATGGACTTCTGA

Alignment

ORF - retro_shar_53 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.2 %
• Parental protein coverage: 99.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ESQRPREEEEDASGGLSEDEDYVPYVPVKQRKQQMLQKLLQMRRKGAAEEEQKDSGSEPRGDEDDIPLGP
          E...P.EEE.D..G.LSE.EDYVPYVPVK.RKQQ.LQ.LLQ.R..G.AEE.QKDSGSE.RGDE.DIPLGP
Retrocopy ERKSPGEEEYDTAGSLSEEEDYVPYVPVKKRKQQKLQTLLQKRWRGEAEEQQKDSGSESRGDEGDIPLGP

Parental  QSNVSLLDQHQHLKEKAEARKESAKEKQLKEEEKILESVAEGRALMSVKEMAKGITYDDPIKTSWKAPRY
          QS.VSLLDQHQ.LKEKA.ARKESAKEKQLKEEEKILESVAEGRALMSVKEMA.GITY.DPIKTSWKAPRY
Retrocopy QSRVSLLDQHQLLKEKANARKESAKEKQLKEEEKILESVAEGRALMSVKEMARGITYKDPIKTSWKAPRY

Parental  VLSMSEARHDRVRKKYHILVEGEGIPPPLKSFKEMKFPAAILRGLKKKGIHHPTPIQIQGIPTILSGRDM
          VLSMS.ARH.RVRKKY.ILVEGEGIPPPLK.FKEMKFPAAILRGLKKKGIHHPTPIQIQGIP..LSGRDM
Retrocopy VLSMSAARHERVRKKYQILVEGEGIPPPLKRFKEMKFPAAILRGLKKKGIHHPTPIQIQGIPAVLSGRDM

Parental  IGIAFTGSGKTLVFTLPVIMFCLEQEKRLPFSKREGPYGLIICPSRELARQTHGILEYYCRLLQEDSSPP
          IGIAFTGSGKTLVFTLP.IMFCLEQE.RLPFSKREGPYGLIICPSRELARQTHGIL.YYC.LLQED..P.
Retrocopy IGIAFTGSGKTLVFTLPLIMFCLEQETRLPFSKREGPYGLIICPSRELARQTHGILDYYCQLLQEDNYPS

Parental  LRCALCIGGMSVKEQMETIRHFSSMMVATPGRLMDLLQKKMVSLDICRYLALDEADRMIDMGFEGDIRTI
          LRCALCIGG.SV.EQMETIRH.....VATPGRLMDLLQKKMV.LD.CRYLALDEADRMIDMGFEGDIRTI
Retrocopy LRCALCIGGTSVREQMETIRHGVHVVVATPGRLMDLLQKKMVNLDVCRYLALDEADRMIDMGFEGDIRTI

Parental  FSYFKGQRQTLLFSATMPKKIQNFAKSALVKPVTINVGRAGAASLDVIQEVEYVKEEAKMVYLLECLQKT
          FSYFKGQRQTLLFSATMP.KIQNFAKSALVKPV..NVGRAGAASLDVIQEVEYVKEE.KMVYLLECLQKT
Retrocopy FSYFKGQRQTLLFSATMPQKIQNFAKSALVKPVIVNVGRAGAASLDVIQEVEYVKEEVKMVYLLECLQKT

Parental  PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGKDQEERTKAIEAFRDGKKDVLVATDVASKGLDFPAI
          PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGG.DQ.ER.KAIE.FRDGKKDVLVATDVASKGLDF..I
Retrocopy PPPVLIFAEKKADVDAIHEYLLLKGVEAVAIHGGRDQAERSKAIETFRDGKKDVLVATDVASKGLDFRDI

Parental  QHVINYDMPEEIENYVHRIGRTGRSGNTGIATTFINKACDESVLMDLKALLLEAKQKVPPVLQVLHCGDE
          QHVINYDMP.EIENYVHRIGRTGRSGNTG.ATTFINKACDESVL.DLKALLLEAKQKVP..LQVLH.GDE
Retrocopy QHVINYDMPVEIENYVHRIGRTGRSGNTGMATTFINKACDESVLLDLKALLLEAKQKVPHMLQVLHRGDE

Parental  SMLDIGGERGCTFCGGLGHRITDCPKLEAMQTKQVSNIGRKDYLAHSSMDF
          SMLDIGGERGCTFCGGLGHRIT.CPKLEAM.TK.VSNIGRKDYLAH.SMDF
Retrocopy SMLDIGGERGCTFCGGLGHRITNCPKLEAMKTKEVSNIGRKDYLAHGSMDF

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_53 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000008770	1 retrocopy	retro_cpor_1521,
Loxodonta africana	ENSLAFG00000026418	1 retrocopy	retro_lafr_689,
Macropus eugenii	ENSMEUG00000014375	1 retrocopy	retro_meug_2040,
Otolemur garnettii	ENSOGAG00000011123	1 retrocopy	retro_ogar_1801,
Rattus norvegicus	ENSRNOG00000012771	1 retrocopy	retro_rnor_2396,
Sarcophilus harrisii	ENSSHAG00000014005	1 retrocopy	retro_shar_53 ,