RetrogeneDB ID: retro_shar_747

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL861726.1:487635..487864(-)
• Located in intron of: ENSSHAG00000008926

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP4
• Ensembl ID: ENSSHAG00000017179
• Aliases: None
• Description: vesicle-associated membrane protein 4 [Source:HGNC Symbol;Acc:12645]

Sequence

>retro_shar_747
ATGCTTCCTAAATTCAAGTGCTACTTAAATGATGATAATGTTATTGGTTTCATGAAAGGTGAAAGGAAAAATCTTTTGGA
AGAAGATTCAGATGAAGATTTTTTTCTCAAAGGGCTCATCTGGACCAAAATTTGGACCTCAGGATGACAAAATTAGGCAT
GTACAGAATCAGGGAAGTGAAGTAATTGATGTCATGCCAGAGAATACTGCAAAAATGATTGAAAGAGGA

Alignment

ORF - retro_shar_747 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.15 %
• Parental protein coverage: 55.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPPKFKRHLNDDDVTGSVKSERRNLLEEDSDEEEDFFLRG-PSGPKFGPRNDKIRHVQNQVDEVIDVMQE
          M.PKFK..LNDD.V.G..K.ER.NLLEEDSDE..DFFL.G..SGPKFGP..DKIRHVQNQ..EVIDVM.E
Retrocopy MLPKFKCYLNDDNVIGFMKGERKNLLEEDSDE--DFFLKG>SSGPKFGPQDDKIRHVQNQGSEVIDVMPE

Parental  NITKVIERG
          N..K.IERG
Retrocopy NTAKMIERG

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_747 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 13 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016956	1 retrocopy	retro_amel_1457,
Choloepus hoffmanni	ENSCHOG00000000124	4 retrocopies	retro_chof_2225, retro_chof_2402, retro_chof_513, retro_chof_58,
Felis catus	ENSFCAG00000013371	1 retrocopy	retro_fcat_1167,
Macropus eugenii	ENSMEUG00000011226	13 retrocopies	retro_meug_1053, retro_meug_115, retro_meug_1257, retro_meug_1406, retro_meug_1489, retro_meug_1587, retro_meug_163, retro_meug_2075, retro_meug_2154, retro_meug_319, retro_meug_386, retro_meug_569, retro_meug_75,
Monodelphis domestica	ENSMODG00000003811	1 retrocopy	retro_mdom_268,
Mustela putorius furo	ENSMPUG00000015609	1 retrocopy	retro_mputfur_315,
Oryctolagus cuniculus	ENSOCUG00000015967	1 retrocopy	retro_ocun_844,
Otolemur garnettii	ENSOGAG00000026745	1 retrocopy	retro_ogar_3369,
Pteropus vampyrus	ENSPVAG00000014342	1 retrocopy	retro_pvam_97,
Sorex araneus	ENSSARG00000001709	2 retrocopies	retro_sara_234, retro_sara_79,
Sarcophilus harrisii	ENSSHAG00000017179	2 retrocopies	retro_shar_584, retro_shar_747 ,
Tupaia belangeri	ENSTBEG00000010829	2 retrocopies	retro_tbel_2607, retro_tbel_4488,
Vicugna pacos	ENSVPAG00000007424	1 retrocopy	retro_vpac_570,