RetrogeneDB ID: retro_itri_227

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393280.1:6936771..6937353(-)
• Located in intron of: ENSSTOG00000026685

Retrocopy information

• Ensembl ID: ENSSTOG00000023018
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHP1
• Ensembl ID: ENSSTOG00000014503
• Aliases: None
• Description: calcineurin-like EF-hand protein 1 [Source:HGNC Symbol;Acc:17433]

Sequence

>retro_itri_227
ATGGGATCTCAGGCCTCTATGTTACTGAGGAATGAAGAATTGGAGGCAATTAAGAAGGAGACTGGCTTTTCCCATAGTCA
GATTGCCCGCCTCTATAGACGGTTCACTACCTTGGACAAAGAAGAGAGTGGATCTCTCAGCCGGGAAGATTTCCAGAGGA
TTCCAGAACTTGCCATCAACCCACTGGGAGACCGGATCATCAGTGCCTTCTTTCCAGATGGAGAAGACCAGGTGAACTTC
CGTGGATTCATAAGAATCTTGGCTCATTTCCGACCCATTGATAATGATGTAAAGAACAAAGATGTGATTGGATCCGAACC
ACTCAATAGCCGAATCAACAAACTACGCTTTGCTTTTCAACTATATGATTTGGATAAAGATGACAAGATCTCCCGCAGTG
AGCTGTTACAGGTGTTACACATGATGGTTGGAGTGAATATCTCAGATGAGCAACTGGGCATCATTGCAGACAGGACCATC
CAGGAAGCTGATCAGGATGGAGATGGAGCCATATCTTTCACAGAATTTGTTAACATTTTAGAGAAGGTGCACATAGAGCA
GAAAATGAGCATTCAATTTCTT

Alignment

ORF - retro_itri_227 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.99 %
• Parental protein coverage: 99.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSRASTLLRDEELEEIKKETGFSHSQITRLYSRFTSLDKGENGTLSREDFQRIPELAINPLGDRIINAF
          MGS.AS.LLR.EELE.IKKETGFSHSQI.RLY.RFT.LDK.E.G.LSREDFQRIPELAINPLGDRII.AF
Retrocopy MGSQASMLLRNEELEAIKKETGFSHSQIARLYRRFTTLDKEESGSLSREDFQRIPELAINPLGDRIISAF

Parental  FPEGEDQVNFRGFMRTLAHFRPIEDNEKSKDVNGPEPLNSRSNKLHFAFRLYDLDKDDKISRDELLQVLR
          FP.GEDQVNFRGF.R.LAHFRPI....K.KDV.G.EPLNSR.NKL.FAF.LYDLDKDDKISR.ELLQVL.
Retrocopy FPDGEDQVNFRGFIRILAHFRPIDNDVKNKDVIGSEPLNSRINKLRFAFQLYDLDKDDKISRSELLQVLH

Parental  MMVGVNISDEQLGSIADRTIQEADQDGDSAISFTEFVKVLEKVDVEQKMSIRFL
          MMVGVNISDEQLG.IADRTIQEADQDGD.AISFTEFV..LEKV..EQKMSI.FL
Retrocopy MMVGVNISDEQLGIIADRTIQEADQDGDGAISFTEFVNILEKVHIEQKMSIQFL

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_227 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_227 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 13 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000009525	1 retrocopy	retro_cfam_2136,
Cavia porcellus	ENSCPOG00000010577	2 retrocopies	retro_cpor_1224, retro_cpor_726,
Homo sapiens	ENSG00000187446	2 retrocopies	retro_hsap_3334, retro_hsap_3541,
Gorilla gorilla	ENSGGOG00000007312	2 retrocopies	retro_ggor_1293, retro_ggor_2392,
Macaca mulatta	ENSMMUG00000017092	2 retrocopies	retro_mmul_1809, retro_mmul_2088,
Mus musculus	ENSMUSG00000014077	4 retrocopies	retro_mmus_1458, retro_mmus_2094, retro_mmus_3133, retro_mmus_3469,
Nomascus leucogenys	ENSNLEG00000003465	4 retrocopies	retro_nleu_1678, retro_nleu_2269, retro_nleu_2608, retro_nleu_2609,
Procavia capensis	ENSPCAG00000005419	1 retrocopy	retro_pcap_240,
Pongo abelii	ENSPPYG00000006370	2 retrocopies	retro_pabe_2749, retro_pabe_2925,
Pan troglodytes	ENSPTRG00000006942	2 retrocopies	retro_ptro_2144, retro_ptro_2407,
Rattus norvegicus	ENSRNOG00000004742	2 retrocopies	retro_rnor_2034, retro_rnor_2223,
Ictidomys tridecemlineatus	ENSSTOG00000014503	1 retrocopy	retro_itri_227 ,
Ictidomys tridecemlineatus	ENSSTOG00000025985	1 retrocopy	retro_itri_1569,