RetrogeneDB ID: retro_itri_421

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393290.1:6223427..6224303(-)
• Located in intron of: ENSSTOG00000006070

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM183A
• Ensembl ID: ENSSTOG00000012466
• Aliases: None
• Description: transmembrane protein 183A [Source:HGNC Symbol;Acc:20173]

Sequence

>retro_itri_421
AATCTCTGTGGTTTGGCAGCCTCTCAGCTTCCTTCAGAGGAAGCTCTTTCTGGGGTTAGTGAGTCCTGTGCCATCATCGA
CAGCAGTGAAGAGATGGATGCCCAGGAGGAAAACATCCATGAGAGAATTGTCTCCAGAAAAAAGAAAAGCAAGAGGCACA
AAGAGGACTTGGACAGGGCTGGAGGAGAAGAGTATCCCATGGATATTTGGTTATTGCTGGCCTCCTACATCCGTCCTGAG
GACATTGTGAATTTTTCCTTGATTTGTAAGAATGCCTGGACTGTCACTTACACTGCTGCCTTTTGGACCAGGTTGTACCG
AAAGCACTACACGCTGGATGCTTCTCTGCCTTTGCGCCTGCGATCAGAGTCAATGGAGAAGCTGCGCTATTTTCGGGCAT
GTGTGATCCATTCTCTGTACCATATGTATGAAACATTTGCTGCTCGAATCTCCAAGAATCCAGCCATTCCAGAAAGCACT
CCCAGCACATTAAAGAATTCCAAATGCTTACTTTTCTGGTGCAGAAAGATTGTTGGGAACAGACAGGAACCAATGTGGGA
ATTCAACTTCAAGTTCAAAAAACAGTCCCCTAGATTAAAGAGCAAATGTATGGAACGATTGCAGCCTCCCATTCAGTATG
AAGATGTTCATACTAACCCAGACCAGGACTGCTGCTTACTGTAGGTCACCACCCTCAATTTCATCTTTATTCCAATTGTC
ATGGGAATGATATTTACCCTGTTTACTATTAATGTGTGCACAGACATGCGGCATCATCAAGTGAAACTGGTGTTCCAAGA
TTCTCCTGTCCATGGTGGTCGGAACCTGCGCAGTGAACAGGGTGTGCAAGTCATCCTGGATCCAGTGCACAGCATC

Alignment

ORF - retro_itri_421 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.15 %
• Parental protein coverage: 94.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLCGLEASQLPAEEALSGVGESCDIIDSSDEMDAQEENIHERTVSRKKKSKRHKEDLDKAGGEEYPMDIW
          .LCGL.ASQLP.EEALSGV.ESC.IIDSS.EMDAQEENIHER.VSRKKKSKRHKEDLD.AGGEEYPMDIW
Retrocopy NLCGLAASQLPSEEALSGVSESCAIIDSSEEMDAQEENIHERIVSRKKKSKRHKEDLDRAGGEEYPMDIW

Parental  LLLASYIRPEDIVNFSLICKNAWTVTCTAAFWTRLYRRHYTLDASLPLRLRPESMEKLRCLRACVIRSLY
          LLLASYIRPEDIVNFSLICKNAWTVT.TAAFWTRLYR.HYTLDASLPLRLR.ESMEKLR..RACVI.SLY
Retrocopy LLLASYIRPEDIVNFSLICKNAWTVTYTAAFWTRLYRKHYTLDASLPLRLRSESMEKLRYFRACVIHSLY

Parental  HMYEPFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSPRLKSKCMERLQPP
          HMYE.FAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSPRLKSKCMERLQPP
Retrocopy HMYETFAARISKNPAIPESTPSTLKNSKCLLFWCRKIVGNRQEPMWEFNFKFKKQSPRLKSKCMERLQPP

Parental  IQYEDVHTNPDQDCCLLQVTTLNFIFIPIVMGMIFTLFTINVSTDMRHHRVRLVFQDSPVHGGRNLRSEQ
          IQYEDVHTNPDQDCCLL.VTTLNFIFIPIVMGMIFTLFTINV.TDMRHH.V.LVFQDSPVHGGRNLRSEQ
Retrocopy IQYEDVHTNPDQDCCLL*VTTLNFIFIPIVMGMIFTLFTINVCTDMRHHQVKLVFQDSPVHGGRNLRSEQ

Parental  GVQVILDPVHSV
          GVQVILDPVHS.
Retrocopy GVQVILDPVHSI

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_421 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_421 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000008318	1 retrocopy	retro_etel_1835,
Felis catus	ENSFCAG00000013106	1 retrocopy	retro_fcat_3,
Homo sapiens	ENSG00000163444	3 retrocopies	retro_hsap_2808, retro_hsap_2863, retro_hsap_3157,
Gorilla gorilla	ENSGGOG00000009834	2 retrocopies	retro_ggor_1358, retro_ggor_2533,
Loxodonta africana	ENSLAFG00000018443	1 retrocopy	retro_lafr_149,
Macaca mulatta	ENSMMUG00000000801	1 retrocopy	retro_mmul_1532,
Nomascus leucogenys	ENSNLEG00000018106	2 retrocopies	retro_nleu_2541, retro_nleu_2663,
Otolemur garnettii	ENSOGAG00000000911	1 retrocopy	retro_ogar_3209,
Pongo abelii	ENSPPYG00000000340	2 retrocopies	retro_pabe_1333, retro_pabe_2627,
Pan troglodytes	ENSPTRG00000001864	2 retrocopies	retro_ptro_1902, retro_ptro_2278,
Rattus norvegicus	ENSRNOG00000003594	2 retrocopies	retro_rnor_1954, retro_rnor_2386,
Sus scrofa	ENSSSCG00000015473	1 retrocopy	retro_sscr_879,
Ictidomys tridecemlineatus	ENSSTOG00000012466	1 retrocopy	retro_itri_421 ,
Tarsius syrichta	ENSTSYG00000007009	1 retrocopy	retro_tsyr_717,