RetrogeneDB ID: retro_itri_1257

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393416.1:1875994..1876624(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPA2
• Ensembl ID: ENSSTOG00000004433
• Aliases: None
• Description: replication protein A2, 32kDa [Source:HGNC Symbol;Acc:10290]

Sequence

>retro_itri_1257
CCAAAGAAATCACGACCAATATGTGAAATAAGAGCCCAAGCCCAGCATATTGTACCCTGTACCATATCTCAGCTGCTTGC
TGCTACTCTGGTTGATGAAGTGTTCAAAATTGGGAATGTGGAAATTTCAAATCACTATTGTGGGAATAATCAGACATTCA
GAGAAGGCTCCAACCAATACTGTTTACAAAATAGATGCATGACAGCTGCACCCATGGATGTTCATCAGTGGGTGGACACA
GATGACACCAGTGGTGAAAATATTGTAGTTCCTCCAGAAACATATGTGAAAGTAGCTGGCCACCTGAGGTCCTTTCAGAA
CAAAAAGATCCTGGGCTTTAAGATCATGCCCCTAGAGGATATGAATGAATTTACCACACATATCCTAGTAGTCAACAAGC
ACATGGTGCTGAGCCAGCCCTCAGAAGGGAAAGCATCTATTCAGCAATCCAGGAATGGGGGAAGCAGGAAGCTTCCATGG
AAATAGCTTCATGCTAACAAATGGCCTCACCAAGGCCCCAAACCAGGTGCTGAATTTGATTAAGGCTTGCCCAGACCTGA
AGGATTGAACTTTCAGAATCTTGGGACCCAGCTCCAACACATGCTTATAGCTTCAATCAAGCAAACTGTG

Alignment

ORF - retro_itri_1257 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.38 %
• Parental protein coverage: 80.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  PTPSQAEKKSRARAQHIVPCTISQLLSATLVDEMF-KIGNVEISQVTIVGIIRHAEKAPTNIVYKIDD-M
          P..S......RA.AQHIVPCTISQLL.ATLVDE.F.K.G.....Q.TIVGIIRH.EKAPTN.VYKID..M
Retrocopy PKKSRPICEIRAQAQHIVPCTISQLLAATLVDEVF>KLGMWKF-QITIVGIIRHSEKAPTNTVYKIDA<M

Parental  TAAPMDVRQWVDTDDTSGENTVVPPETYVKVAGHLRSFQNKKSLVAFKIMPLEDMNEFTTHILEVVNAHM
          TAAPMDV.QWVDTDDTSGEN.VVPPETYVKVAGHLRSFQNKK....FKIMPLEDMNEFTTHIL.VVN.HM
Retrocopy TAAPMDVHQWVDTDDTSGENIVVPPETYVKVAGHLRSFQNKK-ILGFKIMPLEDMNEFTTHIL-VVNKHM

Parental  VLSKSNSQPSVGRASI-SNPGMGEAGNFSGNSFMPTNGLTVVQNQVLNLIKAC-PRPEGLNFQDLRTQLQ
          VLS....QPS.G.ASI.SNPGMGEAG.F.GNSFM.TNGLT...NQVLNLIKAC.PRPEGLNFQ.L.TQLQ
Retrocopy VLS----QPSEGKASI>SNPGMGEAGSFHGNSFMLTNGLTKAPNQVLNLIKAC<PRPEGLNFQNLGTQLQ

Parental  HMPVASIKQAV
          HM..ASIKQ.V
Retrocopy HMLIASIKQTV

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_1257 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1257 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 15 parental genes, and 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000006225	5 retrocopies	retro_btau_1093, retro_btau_1228, retro_btau_1359, retro_btau_406, retro_btau_633,
Callithrix jacchus	ENSCJAG00000009473	1 retrocopy	retro_cjac_225,
Homo sapiens	ENSG00000117748	2 retrocopies	retro_hsap_704, retro_hsap_815,
Gorilla gorilla	ENSGGOG00000015287	2 retrocopies	retro_ggor_599, retro_ggor_668,
Loxodonta africana	ENSLAFG00000014387	1 retrocopy	retro_lafr_519,
Macaca mulatta	ENSMMUG00000018172	2 retrocopies	retro_mmul_1081, retro_mmul_2172,
Nomascus leucogenys	ENSNLEG00000009702	3 retrocopies	retro_nleu_1409, retro_nleu_250, retro_nleu_2511,
Oryctolagus cuniculus	ENSOCUG00000016194	1 retrocopy	retro_ocun_1180,
Otolemur garnettii	ENSOGAG00000015583	2 retrocopies	retro_ogar_1838, retro_ogar_2066,
Pongo abelii	ENSPPYG00000001651	2 retrocopies	retro_pabe_523, retro_pabe_728,
Pan troglodytes	ENSPTRG00000000420	1 retrocopy	retro_ptro_566,
Pteropus vampyrus	ENSPVAG00000001449	1 retrocopy	retro_pvam_166,
Ictidomys tridecemlineatus	ENSSTOG00000004433	2 retrocopies	retro_itri_1257 , retro_itri_773,
Tarsius syrichta	ENSTSYG00000010706	2 retrocopies	retro_tsyr_1184, retro_tsyr_1806,
Tursiops truncatus	ENSTTRG00000007507	1 retrocopy	retro_ttru_873,