RetrogeneDB ID: retro_itri_617

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393306.1:12040382..12040821(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000010285
• Aliases: None
• Description: None

Sequence

>retro_itri_617
GGAAAAATGAGAAAGGTAATTGATGTCATTATATTTTTCGCCAGCTTAGTTTGAAAACATGTAAGTTCAAAGGAGAGACT
TTTGAGAGATTTGCTGAGAAACTAACTCAAATACCTCAAGAAAATATGAAATATCACTGGTATCCAAAAAAACCATCAAA
GGATGGGCCTACAGATGCACCTGTGTTAATAAGCTTCAGAGAGTTAATCTTTGGGTCATAAATGCCTGTGAGAACAGCTG
AATGTTGTACAGTGACCTGGGCTTGCCAAAGGAGCTTACTCTCACAGTGGACCCAGGTGAGTTGCAATGTTGGTATTGGG
AGAAAAGCAATGCATTCATCATTGCCAGCTTTGAAAATGAAGATGAAAACAAGAATGAGATCTCCAAGAAGGTTACCAGG
ACAGTTATCTCTGAGTATCACTTAAGATCCTCTACTTCA

Alignment

ORF - retro_itri_617 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.36 %
• Parental protein coverage: 96.18 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GKMKNEIAAVVFFFTKLVRKHD-KLKKEAVERFAEKLTLILQEKYKNHWYPEKPSK-GQAYRCIRVNKFQ
          GKM......V..FF..LV.KH..K.K.E..ERFAEKLT.I.QE..K.HWYP.KPSK.G.AYRC..VNK.Q
Retrocopy GKMR-KVIDVIIFFASLV*KHV<KFKGETFERFAEKLTQIPQENMKYHWYPKKPSK<GWAYRCTCVNKLQ

Parental  RVDPDVLKACENSCILYSDLGLPKELTLWVDPCEVCCRYGEKNNAFIVASFENEDENKDEISKKVTRALD
          RV...V..ACENS..LYSDLGLPKELTL.VDP.E..C.Y.EK.NAFI.ASFENEDENK.EISKKVTR...
Retrocopy RVNLWVINACENS*MLYSDLGLPKELTLTVDPGELQCWYWEKSNAFIIASFENEDENKNEISKKVTRT--

Parental  KVTSDYHSGSSSS
          .V.S.YH..SS.S
Retrocopy -VISEYHLRSSTS

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_617 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_617 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 9 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000003406	1 retrocopy	retro_cjac_4118,
Dasypus novemcinctus	ENSDNOG00000012987	2 retrocopies	retro_dnov_1703, retro_dnov_2682,
Macaca mulatta	ENSMMUG00000002116	1 retrocopy	retro_mmul_2534,
Mustela putorius furo	ENSMPUG00000010746	1 retrocopy	retro_mputfur_849,
Mus musculus	ENSMUSG00000022863	1 retrocopy	retro_mmus_225,
Otolemur garnettii	ENSOGAG00000013303	8 retrocopies	retro_ogar_1693, retro_ogar_1755, retro_ogar_2575, retro_ogar_2769, retro_ogar_2795, retro_ogar_3346, retro_ogar_524, retro_ogar_551,
Ochotona princeps	ENSOPRG00000012837	1 retrocopy	retro_opri_381,
Ictidomys tridecemlineatus	ENSSTOG00000010285	1 retrocopy	retro_itri_617 ,
Tarsius syrichta	ENSTSYG00000006151	5 retrocopies	retro_tsyr_1172, retro_tsyr_1406, retro_tsyr_1753, retro_tsyr_231, retro_tsyr_495,