RetrogeneDB ID: retro_itri_1044

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393362.1:4202242..4202919(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000028512
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CAPZA1
• Ensembl ID: ENSSTOG00000015956
• Aliases: None
• Description: capping protein (actin filament) muscle Z-line, alpha 1 [Source:HGNC Symbol;Acc:1488]

Sequence

>retro_itri_1044
GAGGATCGGATGTCGGGTGAGGAGAAAGTATGCTTAGCTGCTAAATTCACCACTCATGCACCCCCAGAGGAGTTCAGGGA
AGTATTCAATGATGTCCGGCTACTACTTAACAATGACAAGGAAGGAGCAGCACATGCATTTGCCCAGTATAACATGGACC
AGTTCACACCTGTGAAGACAGAAGGATATGAAGAACAGGTCTTAATTACAGAGCATGGTGACCTGGGGAATAACCAATTT
TTAGATCCAAGAAACAAAATTTCCTTTAAGTTTGATCACTTATGGAAAGAAGCAAATGACCCTCAACCAGAAGAAGTAGA
TGGAGGTTTGAAGTCCTGGAGAGAATCCTGTGACAATGCCTTAAGAGCCTATGTGAAAGATCATTATTACAACGCCTTCT
GTACTGTTTATGCTAAAACTAGAGATGGGCAACAGACTATTATTGCATGTATTAAAAGCCTCCAGTTTCAGCCTAAAAAC
TTTGGAATGGTCGTTGGAGATCAGAGTGGAAGTTCACTATTACACCATCTACAGCCCAGGTGGTTGGAGTGCTCGAGATT
CAGGTTCACTATGATGAAGATGGCCATGTTCAGTTGGTTAATCTTAAAATTGTACAAGATTTAGTAACTGTTTCGAATGA
AGTCCAAACTGCCAAGGAGTTTATTAAAATCATAGAG

Alignment

ORF - retro_itri_1044 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.09 %
• Parental protein coverage: 79.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EDRVSDEEKVRIAAKFITHAPPGEFNEVFNDVRLLLNNDNLLREGAAHAFAQYNMDQFTPVKIEGYEDQV
          EDR.S.EEKV..AAKF.THAPP.EF.EVFNDVRLLLNND....EGAAHAFAQYNMDQFTPVK.EGYE.QV
Retrocopy EDRMSGEEKVCLAAKFTTHAPPEEFREVFNDVRLLLNND---KEGAAHAFAQYNMDQFTPVKTEGYEEQV

Parental  LITEHGDLGNSRFLDPRNKISFKFDHLRKEASDPQPEEVEGGLKSWRESCDNALRAYVKDHYSNGFCTVY
          LITEHGDLGN..FLDPRNKISFKFDHL.KEA.DPQPEEV.GGLKSWRESCDNALRAYVKDHY.N.FCTVY
Retrocopy LITEHGDLGNNQFLDPRNKISFKFDHLWKEANDPQPEEVDGGLKSWRESCDNALRAYVKDHYYNAFCTVY

Parental  AKTIDGQQTIIACIESHQFQPKNF-WNGRWRSEWKFTITPPTAQVVGVLKIQVHYYEDGNVQLVSHKDVQ
          AKT.DGQQTIIACI.S.QFQPKNF.WNGRWRSEWKFTITP.TAQVVGVL.IQVHY.EDG.VQLV..K.VQ
Retrocopy AKTRDGQQTIIACIKSLQFQPKNF<WNGRWRSEWKFTITPSTAQVVGVLEIQVHYDEDGHVQLVNLKIVQ

Parental  DLVTVSNEIQTAKEFIKIIE
          DLVTVSNE.QTAKEFIKIIE
Retrocopy DLVTVSNEVQTAKEFIKIIE

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_1044 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1044 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 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003570	1 retrocopy	retro_amel_219,
Choloepus hoffmanni	ENSCHOG00000004131	8 retrocopies	retro_chof_1008, retro_chof_1419, retro_chof_1499, retro_chof_1704, retro_chof_1861, retro_chof_2129, retro_chof_625, retro_chof_711,
Latimeria chalumnae	ENSLACG00000017963	1 retrocopy	retro_lcha_20,
Myotis lucifugus	ENSMLUG00000009796	1 retrocopy	retro_mluc_2483,
Mustela putorius furo	ENSMPUG00000004977	1 retrocopy	retro_mputfur_616,
Mus musculus	ENSMUSG00000070372	4 retrocopies	retro_mmus_179, retro_mmus_1828, retro_mmus_3370, retro_mmus_349,
Oryctolagus cuniculus	ENSOCUG00000000270	6 retrocopies	retro_ocun_1315, retro_ocun_1417, retro_ocun_1787, retro_ocun_301, retro_ocun_527, retro_ocun_555,
Rattus norvegicus	ENSRNOG00000013538	1 retrocopy	retro_rnor_77,
Sorex araneus	ENSSARG00000001278	1 retrocopy	retro_sara_166,
Ictidomys tridecemlineatus	ENSSTOG00000015956	1 retrocopy	retro_itri_1044 ,
Ictidomys tridecemlineatus	ENSSTOG00000024828	1 retrocopy	retro_itri_1561,
Tarsius syrichta	ENSTSYG00000006259	2 retrocopies	retro_tsyr_179, retro_tsyr_471,
Vicugna pacos	ENSVPAG00000005361	1 retrocopy	retro_vpac_579,