RetrogeneDB ID: retro_shar_836

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL867831.1:36431..36854(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RSL1D1
• Ensembl ID: ENSSHAG00000016705
• Aliases: None
• Description: ribosomal L1 domain containing 1 [Source:HGNC Symbol;Acc:24534]

Sequence

>retro_shar_836
CACCTGCTGGAAAATATTGTTGCTGTGGTGGATGTGCTTTCAGAAAAGTTGCCAAAGAAGTGGGAGAGTGTAACAATTTT
TCACCTGAATACAGAAAAATCTCTTTCTCTTCCAATCTTTTCTTCATTTCTTTTCCATTTGGGTTCTCCAAAAAGTAAGA
AGCAAAAGAATGGCAAAACTGTTGTCACTAAACCTGGCCAGGCTGTAGTGAATCCTGAAAGTGGTTTGGAAGGTCATGAG
CTAGAAACAGAAAAGAAGGGCACAGCAGAGCCTGACTCTTATGATGAGATTCCCCAACTAGTTCCAATCTAAGCATCATC
TCAAAAGTGCCCAAAGCTTGACAAAGCAAGTCGGATAAAGGGTTCTACAGCACAGAGCCTCAGTGCTGAAATAACACAAG
TAAAAAGTCCTGTTAAAAATAGG

Alignment

ORF - retro_shar_836 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.24 %
• Parental protein coverage: 78.8 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  HLVENIFAAVDVLSEKLPEKWESVKYLHLKTEKSLSLPVFSSCVSFLGSPQKSKEENQGNKIATNSLQVS
          HL.ENI.A.VDVLSEKLP.KWESV...HL.TEKSLSLP.FSS....LGSP.KSK....G....T...Q..
Retrocopy HLLENIVAVVDVLSEKLPKKWESVTIFHLNTEKSLSLPIFSSFLFHLGSP-KSKKQKNGKTVVTKPGQAV

Parental  VRPERECGLDDHELEAEKESIAEPDNEDKVPQLVPVQAAFSQKHPELHKAALIKDSTEESINAETSQAKT
          V.P..E.GL..HELE.EK...AEPD..D..PQLVP..A..SQK.P.L.KA..IK.ST..S..AE..Q.K.
Retrocopy VNP--ESGLEGHELETEKKGTAEPDSYDEIPQLVPI*AS-SQKCPKLDKASRIKGSTAQSLSAEITQVKS

Parental  PDEKR
          P...R
Retrocopy PVKNR

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_836 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 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018865	2 retrocopies	retro_cfam_1937, retro_cfam_691,
Choloepus hoffmanni	ENSCHOG00000010827	2 retrocopies	retro_chof_1617, retro_chof_852,
Callithrix jacchus	ENSCJAG00000008375	1 retrocopy	retro_cjac_2154,
Cavia porcellus	ENSCPOG00000010630	3 retrocopies	retro_cpor_1262, retro_cpor_276, retro_cpor_822,
Loxodonta africana	ENSLAFG00000013664	1 retrocopy	retro_lafr_364,
Myotis lucifugus	ENSMLUG00000000784	1 retrocopy	retro_mluc_1309,
Monodelphis domestica	ENSMODG00000029494	2 retrocopies	retro_mdom_1240, retro_mdom_573,
Otolemur garnettii	ENSOGAG00000015151	1 retrocopy	retro_ogar_2604,
Rattus norvegicus	ENSRNOG00000048608	1 retrocopy	retro_rnor_2771,
Sarcophilus harrisii	ENSSHAG00000016705	1 retrocopy	retro_shar_836 ,