RetrogeneDB ID: retro_itri_883

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393338.1:4228049..4228473(+)
• Located in intron of: ENSSTOG00000006213

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000019768
• Aliases: None
• Description: None

Sequence

>retro_itri_883
GTATTTGGGAAAAAAGAGATGTAGATTCTTATGGTGGGTTTGGATGCAGCTGGAAAGACCATCATCTTTTATAAATTGAA
ACTGGAAGAGATTGTGACCACCCTTCCTACAATAGGTTTCAATGTGAAGATAGTAGAATATGGAAATAACAGCTTCACAG
TCTGGGATGTTGGTGGTCAGGACAAAATCAGACCTTTGTGGCAACATTATTTCAAGAACACTCAAGGTCTGATTTTTGTG
GTTTTGGTAATGACAGAGAAAGAGTCAGTGAGACCAAGAAAAAACTAACTAGAATGTTAGTGAAGATGAATTCAGAGATA
GTTTGTTAGTGTTTGTAAATAAACAGAATCTTCCCAGTGCTGTGAATATAGCAGTTATAATAGTCAAGCTTGGCTTACAT
TCCCTTCACCAGAGAAACACATTC

Alignment

ORF - retro_itri_883 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.86 %
• Parental protein coverage: 79.01 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LFGKKEMRILMVGLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNISFTVWDVGGQDKIRPLWRHY
          .FGKKEM.ILMVGLDAAGKT.I.YKLKL.EIVTT.PTIGFNV..VEY.N.SFTVWDVGGQDKIRPLW.HY
Retrocopy VFGKKEM*ILMVGLDAAGKTIIFYKLKLEEIVTTLPTIGFNVKIVEYGNNSFTVWDVGGQDKIRPLWQHY

Parental  FQNTQGLIFVV-DSNDRERVNEAREELTRML-AEDELRDAVLLVFVNKQDLPNAMNAAEITDKLGLHSLR
          F.NTQGLIFVV...NDRERV.E....LTRML..EDE.RD..LLVFVNKQ.LP.A.N.A.I..KLGLHSL.
Retrocopy FKNTQGLIFVV<FGNDRERVSETKKKLTRML<SEDEFRDS-LLVFVNKQNLPSAVNIAVIIVKLGLHSLH

Parental  QRNWY
          QRN..
Retrocopy QRNTF

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_883 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_883 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000004184	1 retrocopy	retro_amel_1639,
Bos taurus	ENSBTAG00000006785	1 retrocopy	retro_btau_26,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
Equus caballus	ENSECAG00000009563	1 retrocopy	retro_ecab_106,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Mus musculus	ENSMUSG00000062421	1 retrocopy	retro_mmus_2056,
Oryctolagus cuniculus	ENSOCUG00000023198	1 retrocopy	retro_ocun_132,
Otolemur garnettii	ENSOGAG00000002503	1 retrocopy	retro_ogar_263,
Ictidomys tridecemlineatus	ENSSTOG00000004295	1 retrocopy	retro_itri_175,
Ictidomys tridecemlineatus	ENSSTOG00000009288	3 retrocopies	retro_itri_1754, retro_itri_273, retro_itri_363,
Ictidomys tridecemlineatus	ENSSTOG00000013990	1 retrocopy	retro_itri_659,
Ictidomys tridecemlineatus	ENSSTOG00000019470	2 retrocopies	retro_itri_1439, retro_itri_1614,
Ictidomys tridecemlineatus	ENSSTOG00000019768	1 retrocopy	retro_itri_883 ,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,