RetrogeneDB ID: retro_shar_778

Retrocopy location

• Organism: Tasmanian devil (Sarcophilus harrisii)
• Coordinates: GL864789.1:456102..456699(+)
• Located in intron of: ENSSHAG00000008598

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHMP1B
• Ensembl ID: ENSSHAG00000016903
• Aliases: None
• Description: charged multivesicular body protein 1B [Source:HGNC Symbol;Acc:24287]

Sequence

>retro_shar_778
ACCATGTCGACCATGGAGAAACACCTCTTCAACCTCAAATTTGCCGCCAAGGAGCTCGGCAGGAGCGCCAAGAAGTGCGA
GAAGGAGGAGAAGGCCGAGAAGGCCAAGATTAAGAAGGCTATCCAAAAGGGTAACACGGAGGTGGCGCGCATCCACGCAG
AGAACGCCATCCGCCAGAAGAACCAGGGCGTTAATTTCTTGAGGTTGAGCGCCCGCGTGGACGCCGTGGCTGCCCGAGTG
CAGACGGCCGTGACCATGGGCAAAGTCACCAAGTCCCTGGCCGGCGTCGTGAAGTCCATGGACGTGGCGCTGAGGAGCAT
GAACCTGGAGAAAATCTCGGCCCTCATGGACAAATTCGAGCACCAGTTCGAGACCCTGGACGTCCAGACGCAGCAGATGG
AAGACACGATGAGCAATACCACCACTCTGACCACGCCGCAAGGCCAAGTGGACCTGCTGCTCCAGGAGATGGCCGATGAA
GCCGGCCTGGATCTCAACATGGAATTGCCCCAGGGCCAGACGGGCTCTGTGGCCACGGTCGCCTCGGCCGAGCAGGATGA
ACTGTCCCAGAGACTGGCTCGTCTGCGCGACCAAGTG

Alignment

ORF - retro_shar_778 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKNLKKEHLFNLKFAAKELNRNAKKCDKEEKAEKTKIKKAIQKGNTEVARIHAENAIRQKNQAINFLRMS
          T......HLFNLKFAAKEL.R.AKKC.KEEKAEK.KIKKAIQKGNTEVARIHAENAIRQKNQ..NFLR.S
Retrocopy TMSTMEKHLFNLKFAAKELGRSAKKCEKEEKAEKAKIKKAIQKGNTEVARIHAENAIRQKNQGVNFLRLS

Parental  ARVDAVAARVQTAVTMGKVTKSMAGVVKSMDATLRSMNLEKISALMDKFEHQFETLDVQTQQMEDTMSST
          ARVDAVAARVQTAVTMGKVTKS.AGVVKSMD..LRSMNLEKISALMDKFEHQFETLDVQTQQMEDTMS.T
Retrocopy ARVDAVAARVQTAVTMGKVTKSLAGVVKSMDVALRSMNLEKISALMDKFEHQFETLDVQTQQMEDTMSNT

Parental  TTLTTPQNQVDMLLQEMADEAGLDLNMELPQGQTGSVGTSVASAEQDELSQRLARLRDQV
          TTLTTPQ.QVD.LLQEMADEAGLDLNMELPQGQTGSV.T.VASAEQDELSQRLARLRDQV
Retrocopy TTLTTPQGQVDLLLQEMADEAGLDLNMELPQGQTGSVAT-VASAEQDELSQRLARLRDQV

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_778 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 16 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000026660	1 retrocopy	retro_cpor_1434,
Equus caballus	ENSECAG00000018625	1 retrocopy	retro_ecab_991,
Gorilla gorilla	ENSGGOG00000025604	1 retrocopy	retro_ggor_1368,
Loxodonta africana	ENSLAFG00000026457	2 retrocopies	retro_lafr_214, retro_lafr_826,
Macropus eugenii	ENSMEUG00000015250	2 retrocopies	retro_meug_1196, retro_meug_205,
Myotis lucifugus	ENSMLUG00000024811	3 retrocopies	retro_mluc_1161, retro_mluc_1344, retro_mluc_673,
Monodelphis domestica	ENSMODG00000004273	2 retrocopies	retro_mdom_1444, retro_mdom_154,
Mus musculus	ENSMUSG00000031242	1 retrocopy	retro_mmus_1735,
Ochotona princeps	ENSOPRG00000018556	1 retrocopy	retro_opri_577,
Pongo abelii	ENSPPYG00000020505	1 retrocopy	retro_pabe_1581,
Pteropus vampyrus	ENSPVAG00000001416	2 retrocopies	retro_pvam_208, retro_pvam_59,
Rattus norvegicus	ENSRNOG00000002323	2 retrocopies	retro_rnor_1361, retro_rnor_623,
Sarcophilus harrisii	ENSSHAG00000016903	2 retrocopies	retro_shar_776, retro_shar_778 ,
Tarsius syrichta	ENSTSYG00000011727	1 retrocopy	retro_tsyr_1611,
Tursiops truncatus	ENSTTRG00000008066	2 retrocopies	retro_ttru_1002, retro_ttru_235,
Vicugna pacos	ENSVPAG00000000854	2 retrocopies	retro_vpac_112, retro_vpac_422,