RetrogeneDB ID: retro_itri_864

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393334.1:2827335..2827850(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000028389
• Aliases: None
• Description: None

Sequence

>retro_itri_864
ATTGATGAACTCCCAGAGGGAGCGATAAAGCCTCCAGCAAACAAGGATCCTATCTCCTTTTTTGGCACTCATGAAATTGT
GTTTCTAGGTCCCAAAGACCTTTTTCCATAGAAGGAATAGAAAGACAAGTTTGGGAAGTCAAGCAAACGGAAAGGATTTG
ATGAAGGATTGTGGGACATAGAAAATAACCCAGGTGTCAGGTTCACTGGATACCTAGAAATTTGGCACAGAGCTCCTCAG
AAACTGAGGGAGAAGGTGGAAACACTTCAGATGCAAGCAGTGAGGAAGAAGGCCACAGAGTAGAAGAAGATGAGAGAGGT
AAAAGAAAAAATGCAAAAGGGGGCTCCAAAGGGAAAAACTCACATACATCAAAGAAATCCTCTGAACAATCCTGGAAATC
TCGAGGAGATGCAGATGATAAAGATTGCAAAGAAGAAAACAAAGACAGCTCTGAGGATGGAGATGCTGACAATGACACAA
GGACCACTTCACATTTGCAGAAAACCAGTGAAGGG

Alignment

ORF - retro_itri_864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.57 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IDELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKDKFGKSNKRKGFNEGLWEIENNPGVKFTG
          IDELPEGA.KPPANK.PI.FFGTHE..FLGPKDLFP.KE.KDKFGKS.KRKGF.EGLW.IENNPGV.FTG
Retrocopy IDELPEGAIKPPANKDPISFFGTHEIVFLGPKDLFP*KE*KDKFGKSSKRKGFDEGLWDIENNPGVRFTG

Parental  YQAIQQ-QSSSETEGEGGNTADASSEEEGDRVEEDGKGKRKNEKGGSKRKKSYTSKKSSKQSRKSPGDED
          Y..I...QSSSETEGEGGNT.DASSEEEG.RVEED..GKRKN.KGGSK.K.S.TSKKSS.QS.KS.GD.D
Retrocopy YLEIWH<QSSSETEGEGGNTSDASSEEEGHRVEEDERGKRKNAKGGSKGKNSHTSKKSSEQSWKSRGDAD

Parental  DKDCKEEENKSSSEGGDAGNDTRNTTSDLQKTSEG
          DKDCK.EENK.SSE.GDA.NDTR.TTS.LQKTSEG
Retrocopy DKDCK-EENKDSSEDGDADNDTR-TTSHLQKTSEG

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_864 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_864 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018527	1 retrocopy	retro_btau_1740,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234,
Loxodonta africana	ENSLAFG00000002512	1 retrocopy	retro_lafr_676,
Ictidomys tridecemlineatus	ENSSTOG00000028389	2 retrocopies	retro_itri_292, retro_itri_864 ,
Tursiops truncatus	ENSTTRG00000004950	1 retrocopy	retro_ttru_1471,
Vicugna pacos	ENSVPAG00000004599	1 retrocopy	retro_vpac_380,