RetrogeneDB ID: retro_shar_181

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834567.1:455433..456225(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELOVL1
• Ensembl ID: ENSSHAG00000001806
• Aliases: None
• Description: ELOVL fatty acid elongase 1 [Source:HGNC Symbol;Acc:14418]

Sequence

>retro_shar_181
CAGTTGAAGAAGAGAGCAGACCCCGGCTGCAGGACTACCCTCTGATGGACACCCCGTTGCTCATGACCTCCATCTTTGTT
GGCTATATCTATTTTGTGCTGTCCCTTGGGCCCCAGCTGATGGCCAATCGAAAGCCATTCCAGTTTCACAGCTTCATAGT
CGTATACAACTTCTCTCTGGTAGTTCTCTTCCTCTACATAGTCTATGAGTTCCTGATGTCTGGCTGGCCGAGCACCTACA
CATGGCGTTGTGACCCTATGGACTATTCCCAGAACGCAAAGGCCCTCTGGATGGTTTGTGTGGCTTAGCTCTTTCTCTTC
TCCAAGTTCATCGAGTTGATGGACACAGTAATCTTGATTCTTCAAAAGAAGAATGGCCAGGTGAGTTTCTTGCATGTCTT
TCATCAATCAACCCTGGAGCTGGTGGTGGGGCGTTAGGGTGGCCCCAGGAGGAATGGGTTCCTTTCATGCCACGGTGAAC
TCCTCTGTGCATGTGATCATGTACCTTTATTATGGGCTGTCCACTTTGGGCCTGGCCGCCCAGCCCTATCTCTGGTGGAA
GCACATGACAGCCATCCATCTGATCCAGTTTGTGCTGGTCTTGCTGCACATCTCTCAGTATTACTTCCTGCCCAGCTGTG
ACTACCAGTACCCTGTAATCATTCACCTCATCTGGATGTACAGGACCATCTTACTTGTGCTCTTCTCCAACTTCTGGTAC
CAATCGTACACCAAAGGCAAGTGGCTGCCAAGGACTGCCCAGCAGAAAGGGGTGCCCAAAGTCAAGGTGAAC

Alignment

ORF - retro_shar_181 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.9 %
• Parental protein coverage: 96.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EVMKRADP-RLQGYPLMDTPLLMTSILIGYVYFVLSLGPRLMANRKPFQLRGFMVVYNFSLVALSLYIVY
          ...KRADP.RLQ.YPLMDTPLLMTSI..GY.YFVLSLGP.LMANRKPFQ...F.VVYNFSLV.L.LYIVY
Retrocopy QLKKRADP<RLQDYPLMDTPLLMTSIFVGYIYFVLSLGPQLMANRKPFQFHSFIVVYNFSLVVLFLYIVY

Parental  EFLMSGWLSTYTWRCDPVDYSQNPEALRMVRVAWLFLFSKFIELMDTVIFILRKKDGQVTFLHVFHHSVL
          EFLMSGW.STYTWRCDP.DYSQN..AL.MV.VA.LFLFSKFIELMDTVI.IL.KK.GQV.FLHVFH.S.L
Retrocopy EFLMSGWPSTYTWRCDPMDYSQNAKALWMVCVA*LFLFSKFIELMDTVILILQKKNGQVSFLHVFHQSTL

Parental  -PWSWWWGVRVAPGGMGSFHAMVNSSVHVIMYLYYGLSALGPAAQPYLWWKKHMTAIQLIQFVLVSLHIS
          ..W..WWGVRVAPGGMGSFHA.VNSSVHVIMYLYYGLS.LG.AAQPYLWW.KHMTAI.LIQFVLV.LHIS
Retrocopy >SW--WWGVRVAPGGMGSFHATVNSSVHVIMYLYYGLSTLGLAAQPYLWW-KHMTAIHLIQFVLVLLHIS

Parental  QYYFLPSCDYQYPVIIHLIWMYGTIFFVLFSNFWYQSYTKGKRLPKAAQQNGVPKVKAN
          QYYFLPSCDYQYPVIIHLIWMY.TI..VLFSNFWYQSYTKGK.LP..AQQ.GVPKVK.N
Retrocopy QYYFLPSCDYQYPVIIHLIWMYRTILLVLFSNFWYQSYTKGKWLPRTAQQKGVPKVKVN

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_181 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Sarcophilus harrisii	ENSSHAG00000001806	1 retrocopy	retro_shar_181 ,