RetrogeneDB ID: retro_itri_720

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393314.1:1161362..1161793(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: VAMP7
• Ensembl ID: ENSSTOG00000025036
• Aliases: None
• Description: vesicle-associated membrane protein 7 [Source:HGNC Symbol;Acc:11486]

Sequence

>retro_itri_720
ATGGCCATTCTTTTTGCTGTTGTTGCCAGGGGATCCACTATACTTGCCAAACATGCTTGGTGTGAAGGAAACTTCCTGGA
GGTGATAGAGCAGATTCTGGTTAAGATACCTTCTGAAAATAACAAACTAATATACTCACATGGTAATTATTTGTTTCATT
ACATCTGCCAAGACAGGATTCTATGTCTTTGTATCACTGATGATGACTTTGAACGTTCCGGAGCCTTCAATTTTTTGAAT
GAGGTAAAGAAGAGGTTTCAGACAACTTATGGCTCAAGGGCACAGACAGCACATCCATATGCCATGAATAGTGAGTTCTC
AAGTGTCTTGGCTGCACAATTGAAGCATCATTCTGAGAATAAGGGCCTAGACAAAGTGATGGAGACTCAAGCCTAGTGGA
TGAACTGAAGGGAATCATGGTCAGAAACATA

Alignment

ORF - retro_itri_720 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAILFAVVARGTTILAKHAWCGGNFLEVTEQILAKIPSENNKLTYSHGNYLFHYICQDRIVYLCITDDDF
          MAILFAVVARG.TILAKHAWC.GNFLEV.EQIL.KIPSENNKL.YSHGNYLFHYICQDRI..LCITDDDF
Retrocopy MAILFAVVARGSTILAKHAWCEGNFLEVIEQILVKIPSENNKLIYSHGNYLFHYICQDRILCLCITDDDF

Parental  ERSRAFNFLNEVKKRFQTTYGSRAQTALPYAMNSEFSSVLAAQLKHHSENKGLDKVMETQA-QVDELKGI
          ERS.AFNFLNEVKKRFQTTYGSRAQTA.PYAMNSEFSSVLAAQLKHHSENKGLDKVMETQA..VDELKGI
Retrocopy ERSGAFNFLNEVKKRFQTTYGSRAQTAHPYAMNSEFSSVLAAQLKHHSENKGLDKVMETQA<LVDELKGI

Parental  MVRNI
          MVRNI
Retrocopy MVRNI

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Ictidomys tridecemlineatus was not studied using RNA-Seq expression data.

ChIP-Seq

Ictidomys tridecemlineatus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_itri_720 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_720 was not experimentally validated.

Homology

Retrocopy orthology:

Ictidomys tridecemlineatus 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000016289	2 retrocopies	retro_cjac_1958, retro_cjac_2410,
Cavia porcellus	ENSCPOG00000024405	1 retrocopy	retro_cpor_714,
Mus musculus	ENSMUSG00000051412	1 retrocopy	retro_mmus_2131,
Oryctolagus cuniculus	ENSOCUG00000001270	1 retrocopy	retro_ocun_842,
Pteropus vampyrus	ENSPVAG00000000829	1 retrocopy	retro_pvam_513,
Ictidomys tridecemlineatus	ENSSTOG00000025036	1 retrocopy	retro_itri_720 ,
Tursiops truncatus	ENSTTRG00000010643	1 retrocopy	retro_ttru_66,