RetrogeneDB ID: retro_itri_259

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393281.1:4801672..4802056(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000024989
• Aliases: None
• Description: None

Sequence

>retro_itri_259
GTGAGCAGCAAAGAAGAATGGAGAGGTTTCAGAAGAAGAAACACAACAACTTCCCTGTACAACCAAAGGGAGGGGAAGGA
TGTTAGTTCACCTTCACCCATGATGCTGGCCTTCAAGTCATTTCAGCAGGAATTGGATGTGAGGCATGACAAACATGAGA
GACTTGTGAAACTTGGTTGGGATATAACTGTTGAACATAAGAGGACGATTGTTCTCCTCCATAGGATTACAAGTGCTCCT
GATAATGGAAGAAATATTGACTAAATCCTAAATTATATTAGATGGTATCAGACAAAAAATATGACAGGTAGCCCAAGAGC
TATCAGGAGATCAGTTCCACTTAGCTGTCACTCAGGATTGTAGGAATATGTGCTATCTCTTTCC

Alignment

ORF - retro_itri_259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.91 %
• Parental protein coverage: 80. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSGKEGPGGFRKRKHDNFPHGQRREGKDVSASSPVMLAFKSFQQELDARHDKYERLVKLSRDITVESKRT
          .S.KE...GFR.R........QR.EGKDVS..SP.MLAFKSFQQELD.RHDK.ERLVKL..DITVE.KRT
Retrocopy VSSKEEWRGFRRRNTTTSLYNQR-EGKDVSSPSPMMLAFKSFQQELDVRHDKHERLVKLGWDITVEHKRT

Parental  IFLLHRITSAPD-MEEILTESEVKLDGVRQKILQVAQELSGEDMHQFHRAIT-TGLQEYVEAVS
          I.LLHRITSAPD.MEEILT.S...LDG.RQKI.QVAQELSG....QFH.A.T..GL.EYV...S
Retrocopy IVLLHRITSAPD>MEEILTKS*IILDGIRQKI*QVAQELSGD---QFHLAVT<SGL*EYVLSLS

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_259 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_259 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002637	1 retrocopy	retro_amel_1655,
Dasypus novemcinctus	ENSDNOG00000006963	1 retrocopy	retro_dnov_1829,
Felis catus	ENSFCAG00000028088	1 retrocopy	retro_fcat_1789,
Myotis lucifugus	ENSMLUG00000015591	1 retrocopy	retro_mluc_1131,
Mus musculus	ENSMUSG00000056820	1 retrocopy	retro_mmus_393,
Otolemur garnettii	ENSOGAG00000005575	1 retrocopy	retro_ogar_91,
Ictidomys tridecemlineatus	ENSSTOG00000024989	1 retrocopy	retro_itri_259 ,