RetrogeneDB ID: retro_itri_342

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393285.1:7872809..7873439(+)
• Located in intron of: ENSSTOG00000011536

Retrocopy information

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

Parental gene information

• Parental gene symbol: CAPNS1
• Ensembl ID: ENSSTOG00000026235
• Aliases: None
• Description: calpain, small subunit 1 [Source:HGNC Symbol;Acc:1481]

Sequence

>retro_itri_342
ATCGTGGGGGGCCTTGTGAACCTGATCAGCGAGGCTGCTGCCGCTCAGTATACCCCGGAGCCGCCGCCGCCCACCCAGCA
GCACTTCACCACCGTGGAAGCCTCGGAGAGCGAGGAGGTGAGGCGTTTTCGGCACCAGTTTGCGCAGCTGGCTGGACCCG
ACATGGAGGTGGGTGCCACTGACCTGATGAACATTCTCAACAAAGTCCTGGCTAAGCACAAGTATCTGAACACCGCCAGA
TTTAGCCTGGACACCTGCCGCAGCATCGTGTCTGTCATGGACAGCGACACCACGGGGAAGCTGGGCTTCGAGGAGTTCAA
GTATCTGTGGAACAACATCAAGAAGTGGCAGTGCGTCTACCTGCAGTACGTCAGGGACGGTTCCGGGTCTCTGGGGAGCT
CCCAGCTGCGGGAAGCTCTGCAGGCAGCGGGCTTCCAGCTGAACGAACAGCTTTACCAGATGATCCTCCGCCGTTACGTC
GACGAGGACCGGGGCATGGACTTCAACGACTTCATCAGCTGCCTGGTCCGCCTGGACGCCATGTTCCGTGCCTTCAAGTC
CCTGGACAGAGATGCAGATGGCCTGATTCAGGTGTCCATCCAAGAATGGCTGCAGCTGACCATGTATTCC

Alignment

ORF - retro_itri_342 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 78.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ILGGVISAISEAAA-QYNPEPPPP-RTHYSNIEANESEEVRQFRKLFAQLAGDDMEVSATELMNILNKIV
          I.GG....ISEAAA.QY.PEPPPP...H....EA.ESEEVR.FR..FAQLAG.DMEV.AT.LMNILNK..
Retrocopy IVGGLVNLISEAAAAQYTPEPPPPTQQHFTTVEASESEEVRRFRHQFAQLAGPDMEVGATDLMNILNKVL

Parental  TRHPDLKTDGFGIDTCRSMVAVMDSDTTGKLGFEEFKYLWNNIKKWQAIYKQFDFDRSGTICSSELPGAF
          ..H..L.T..F..DTCRS.V.VMDSDTTGKLGFEEFKYLWNNIKKWQ..Y.Q...D.SG...SS.L..A.
Retrocopy AKHKYLNTARFSLDTCRSIVSVMDSDTTGKLGFEEFKYLWNNIKKWQCVYLQYVRDGSGSLGSSQLREAL

Parental  EAAGFRLNDHLYNMIIRRYSDEEGNMDFDNFISCLVRLDAMFRAFKSLDRDGTGQIQVNIQEWLQLTMYS
          .AAGF.LN..LY.MI.RRY.DE...MDF..FISCLVRLDAMFRAFKSLDRD..G.IQV.IQEWLQLTMYS
Retrocopy QAAGFQLNEQLYQMILRRYVDEDRGMDFNDFISCLVRLDAMFRAFKSLDRDADGLIQVSIQEWLQLTMYS

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_342 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_342 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 25 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000000511	1 retrocopy	retro_acar_205,
Ailuropoda melanoleuca	ENSAMEG00000001024	1 retrocopy	retro_amel_136,
Bos taurus	ENSBTAG00000014872	2 retrocopies	retro_btau_1126, retro_btau_692,
Canis familiaris	ENSCAFG00000031314	1 retrocopy	retro_cfam_942,
Callithrix jacchus	ENSCJAG00000009594	1 retrocopy	retro_cjac_2940,
Cavia porcellus	ENSCPOG00000000115	1 retrocopy	retro_cpor_1131,
Equus caballus	ENSECAG00000012210	1 retrocopy	retro_ecab_707,
Felis catus	ENSFCAG00000014149	1 retrocopy	retro_fcat_1691,
Homo sapiens	ENSG00000126247	1 retrocopy	retro_hsap_98,
Gorilla gorilla	ENSGGOG00000003699	2 retrocopies	retro_ggor_1241, retro_ggor_263,
Myotis lucifugus	ENSMLUG00000024944	1 retrocopy	retro_mluc_2336,
Macaca mulatta	ENSMMUG00000000249	2 retrocopies	retro_mmul_1334, retro_mmul_1567,
Monodelphis domestica	ENSMODG00000014179	1 retrocopy	retro_mdom_410,
Mustela putorius furo	ENSMPUG00000005617	1 retrocopy	retro_mputfur_444,
Mus musculus	ENSMUSG00000001794	1 retrocopy	retro_mmus_80,
Nomascus leucogenys	ENSNLEG00000011712	2 retrocopies	retro_nleu_1328, retro_nleu_992,
Pongo abelii	ENSPPYG00000009898	2 retrocopies	retro_pabe_1359, retro_pabe_448,
Pelodiscus sinensis	ENSPSIG00000012793	1 retrocopy	retro_psin_45,
Pan troglodytes	ENSPTRG00000010887	2 retrocopies	retro_ptro_1112, retro_ptro_168,
Pteropus vampyrus	ENSPVAG00000012885	3 retrocopies	retro_pvam_1375, retro_pvam_639, retro_pvam_737,
Rattus norvegicus	ENSRNOG00000045747	2 retrocopies	retro_rnor_1447, retro_rnor_2145,
Sorex araneus	ENSSARG00000004266	1 retrocopy	retro_sara_215,
Sus scrofa	ENSSSCG00000030149	2 retrocopies	retro_sscr_495, retro_sscr_73,
Ictidomys tridecemlineatus	ENSSTOG00000026235	1 retrocopy	retro_itri_342 ,
Vicugna pacos	ENSVPAG00000008074	1 retrocopy	retro_vpac_64,