RetrogeneDB ID: retro_shar_142

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL834462.1:450224..450711(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD7
• Ensembl ID: ENSSHAG00000006762
• Aliases: None
• Description: COMM domain containing 7 [Source:HGNC Symbol;Acc:16223]

Sequence

>retro_shar_142
CATCCCAACCAACTTGAGCCAGCTCAATGAGAGCAGGTTGCAGTGCTAAGCTCAGTGATTTTCTGCCTCTTGGTTCAATC
TAAGGAGATTGACACATTCTTGGCTAAATTGTCTGATTTTGCTACCACCAATTAGATCAGCCTTGGGCCCCAAAGGAACA
ACATGAAAAAGCCTTCTCCTAGGGCCTAATGGTGCCTTGAAGAAGAATATGACTGCCGAGCAGGTTGGAGCAGATTTCAT
TACTCTGGGGCTCAGTGAAGAGAAAGTCACTTATTTTTTCTGAGAAGTAGAAGCAGAAATTTCCACACTTGCTGTATGGG
CAATAGGACAGAAATTGATGATTAGCCAGATTATAGATATGGAAGAAAATGTGGAGTGACATCAGGGAGCAATGAACTGA
AGAAAGAAGGGATTTTTTTTTTTACAATTGAAGTTCGTGGTTAAAAAAGAAAACCAGTCTGAAAACATATAGAGAGAGTT
AACCTTG

Alignment

ORF - retro_shar_142 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.86 %
• Parental protein coverage: 79.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  HLNQLSA---EQFSTLTEVIFYFLIQPKEIETFLAKLSDFAATNQISLGPLKNIVK-SILLVPNGALKKN
          H.NQL.....EQ...L..VIF..L.Q.KEI.TFLAKLSDFA.TN.ISLGP..N..K.S.LL.PNGALKKN
Retrocopy HPNQLEPAQ*EQVAVLSSVIFCLLVQSKEIDTFLAKLSDFATTN*ISLGPQRNNMK>SLLLGPNGALKKN

Parental  MTAEQVRADFITLGLSEEKATY-FSEKWKQK-SSTLARWAIGQTLMINQLIDME-WKFGVTSGSSEL-QK
          MTAEQV.ADFITLGLSEEK.TY.FSEK.KQK..STLA.WAIGQ.LMI.Q.IDME..K.GVTSGS.EL..K
Retrocopy MTAEQVGADFITLGLSEEKVTY>FSEK*KQK<ISTLAVWAIGQKLMISQIIDME<RKCGVTSGSNEL>RK

Parental  VGSIFLQLKLVVKKGNQTENVYIELTL
          .G....QLK.VVKK.NQ.EN...ELTL
Retrocopy KGXXXXQLKFVVKKENQSENI*RELTL

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_142 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 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000008561	2 retrocopies	retro_chof_1254, retro_chof_345,
Loxodonta africana	ENSLAFG00000008789	1 retrocopy	retro_lafr_1194,
Macropus eugenii	ENSMEUG00000010627	1 retrocopy	retro_meug_1062,
Monodelphis domestica	ENSMODG00000019450	3 retrocopies	retro_mdom_1047, retro_mdom_313, retro_mdom_890,
Sarcophilus harrisii	ENSSHAG00000006762	1 retrocopy	retro_shar_142 ,
Ictidomys tridecemlineatus	ENSSTOG00000006640	1 retrocopy	retro_itri_311,