RetrogeneDB ID: retro_itri_380

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393287.1:12928411..12928964(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000023222
• Aliases: None
• Description: None

Sequence

>retro_itri_380
CAGCAGACGATGATCAGATGCTTCACACCAATCCAGCCTCAAAGGCCCTTTGTTTTCCAACATTGCTGTCACATTCGGCC
ATTTCTCTTTATTTCACATGGCAGAAAATATATGTTTTGTGGAGCTTTTCCTCCAGCACAGAGAATGTGCTGAGTCAAGA
GCAGTTCTGGCAGCATATCTAGCTGTTTCTAAATTTGTCAATAGTGTCTGTCAAGTTGCCACAGAAACATTCGGACCTCC
TCTCAGTGCATCAGGTATGATCATGACTGTGCCCACAGGGGTCGGCACTAAGATCCCGAAAGCAGAGCTCACCATCACCT
TCCTCCCAGGGCTCACAACAGGGAATGCCCTAAAAGCCATTATTGCCATGGATCCAGCCAGAACCATCCTGAGATGGAAA
TGTTTTGATCATGCAGCCCATCTTAGGGGAGTTTTCTTCAGCATATGGTATATTATTTATGGTCATGAACTATTTTGGAA
GAATAGGTAGCCTCAAGTGAAAATCTGGCATGAAATGAAAACTGATAGTCCCCAAAAAGGAGGCGGCTCTAAG

Alignment

ORF - retro_itri_380 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.66 %
• Parental protein coverage: 91.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QRTMMRYFT-SNPASKVLCSPMLLSTFSHFSLFHMAANMYVLWSFSSSIVNILGQEQF-MAVYLSAGVIS
          Q.TM.R.FT..NPASK.LC.P.LLS..S..SL.......YVLWSFSSS..N.L.QEQF..A.YL.....S
Retrocopy QQTMIRCFT<TNPASKALCFPTLLS-HSAISLYFTWQKIYVLWSFSSSTENVLSQEQF<LAAYLA---VS

Parental  NFVSYMCKVATGRYGPSLGASGAIMSVLAAVCTKIPEGRLAIIFLPMFTFTAGNALKAIIAMDTAGMILG
          .FV...C.VAT...GP.L.ASG.IM.V...V.TKIP...L.I.FLP....T.GNALKAIIAMD.A..IL.
Retrocopy KFVNSVCQVATETFGPPLSASGMIMTVPTGVGTKIPKAELTITFLP--GLTTGNALKAIIAMDPARTILR

Parental  WKFFDHAAHLGGALFGIWYITYGHELIWKNREPLVKMWHEMRTDGPKKGGGSK
          WK.FDHAAHL.G..F.IWYI.YGHEL.WKNR.P.VK.WHEM.TD.P.KGGGSK
Retrocopy WKCFDHAAHLRGVFFSIWYIIYGHELFWKNR*PQVKIWHEMKTDSPQKGGGSK

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_380 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_380 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 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000021241	2 retrocopies	retro_cjac_1415, retro_cjac_2384,
Dipodomys ordii	ENSDORG00000014935	1 retrocopy	retro_dord_315,
Homo sapiens	ENSG00000175193	1 retrocopy	retro_hsap_3526,
Gorilla gorilla	ENSGGOG00000000416	1 retrocopy	retro_ggor_2384,
Myotis lucifugus	ENSMLUG00000004507	1 retrocopy	retro_mluc_883,
Mus musculus	ENSMUSG00000033918	2 retrocopies	retro_mmus_1882, retro_mmus_3526,
Nomascus leucogenys	ENSNLEG00000006072	1 retrocopy	retro_nleu_491,
Oryctolagus cuniculus	ENSOCUG00000007882	1 retrocopy	retro_ocun_541,
Otolemur garnettii	ENSOGAG00000006126	1 retrocopy	retro_ogar_648,
Pongo abelii	ENSPPYG00000014338	2 retrocopies	retro_pabe_2290, retro_pabe_2912,
Pan troglodytes	ENSPTRG00000015673	1 retrocopy	retro_ptro_2394,
Ictidomys tridecemlineatus	ENSSTOG00000023222	1 retrocopy	retro_itri_380 ,