RetrogeneDB ID: retro_itri_1839

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH394004.1:120016..120390(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000026117
• Aliases: None
• Description: None

Sequence

>retro_itri_1839
ATGCCCAAGAATAAAGGTGAAGGAGGTGAAAACAGGCAGAGGAAGGAATAAGAATGGGTCTGAAGAAAGAGTTGGTGTTC
AAAAGGGCGGGCAAGAGTGTGCTCAGGGAATCAGAATGATGGGAAATGGACCATTAGAAGCAATGAATTTCAATGGTGTG
AAGAGGTTTGTCACATCAGAGGAAAATTGAGAAAAAAGGTGTGGAGAAATACACCAGACATTATATTGGTTGTTCTCTAA
GACAACCAGAATAACAAATCTGATGTAATTTTAAAATACAAAGCAAATTGAAGCTAGAAGTTGAGGTTTACTGACAGCTT
CTGGAGCAGCCTAAAATCAATGAGCCTGATACATATGGTCCTGGAGATGATGAA

Alignment

ORF - retro_itri_1839 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.08 %
• Parental protein coverage: 88.19 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPKNKGKGGKNRR-RGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKR-LCHIRGKLRKK
          MPKNKG..G...R.RG.N.N.SE.R..V.K..GQE.AQ.I.M.GNG.LEAM.F.GVKR..CHIRGKLRKK
Retrocopy MPKNKGE-GGENR>RGRNKNGSEERVGVQK-GGQECAQGIRMMGNGPLEAMNFNGVKR<VCHIRGKLRKK

Parental  VWINTSDIILVGLRDYQDNKADVILKYNADEARSLK-AYGELPEHAKINETDTFGPGDDD
          VW.NT.DIILV.L.D.Q.NK.DVILKY.A.....L...Y..L.E..KINE.DT.GPGDD.
Retrocopy VWRNTPDIILVVL*DNQNNKSDVILKYKAN*S*KLR<VY*QLLEQPKINEPDTYGPGDDE

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_1839 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1839 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.

---

Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Equus caballus	ENSECAG00000006469	2 retrocopies	retro_ecab_464, retro_ecab_634,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Ictidomys tridecemlineatus	ENSSTOG00000026117	1 retrocopy	retro_itri_1839 ,