RetrogeneDB ID: retro_itri_574

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393302.1:14926627..14926996(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TXNDC17
• Ensembl ID: ENSSTOG00000021986
• Aliases: None
• Description: thioredoxin domain containing 17 [Source:HGNC Symbol;Acc:28218]

Sequence

>retro_itri_574
ATGGCTATCTTCAAGGAGGGGAGCATGTTGGGCTTTGAGGAGTTCAATCAGGCTGTGAAACAACACCTCGGCAAGACCAT
TTTGCCTACTTTACAGGTTCTAAGGACACCGAAGGGAAAAGCTGGTGTCCCAAATGTGTGCAGGCAGAACCAGTCATTTG
AGAGGGGCTGAAAGCATATTAGTATAGAATATATGTTCATCCACTGCCAAGTAGGAGAAAAAATCTTATTGAAAAGATTC
AAATAATGACTTAAGAAAACAACTGAAAGTAACTGCAGTGCCTACACTACTTAAATGTGGAACCTTCAAAAACTGGTATA
ATCTGAGTGTTTTCAGGCCAACCTTGTGGTGATGCTGTTCTCTGAAGAT

Alignment

ORF - retro_itri_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.74 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MAIYEEVSVSGFEEFNQAVKQHLGKTI-FAYFTGSKDAEGKSWCPDCVQAEPVVREGL-KHVSKECVFIH
          MAI..E.S..GFEEFNQAVKQHLGKTI.FAYFTGSKD.EGKSWCP.CVQAEPV..EGL.KH.S.E..FIH
Retrocopy MAIFKEGSMLGFEEFNQAVKQHLGKTI<FAYFTGSKDTEGKSWCPKCVQAEPVI*EGL>KHISIEYMFIH

Parental  CQVGE-KPYWKDPNNDFRKQLKVTAVPTLIKYGT-PQKLVESECLQANLVEMLFSED
          CQVGE.K.Y.KD.NND.RKQLKVTAVPTL.K.GT..QKLV.SEC.QANLV.MLFSED
Retrocopy CQVGE>KSY*KDSNNDLRKQLKVTAVPTLLKCGT<LQKLV*SECFQANLVVMLFSED

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_574 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_574 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 27 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000007038	4 retrocopies	retro_amel_1181, retro_amel_1267, retro_amel_148, retro_amel_344,
Callithrix jacchus	ENSCJAG00000011150	4 retrocopies	retro_cjac_2775, retro_cjac_2877, retro_cjac_2887, retro_cjac_3048,
Cavia porcellus	ENSCPOG00000002887	1 retrocopy	retro_cpor_116,
Equus caballus	ENSECAG00000025006	1 retrocopy	retro_ecab_430,
Echinops telfairi	ENSETEG00000001905	1 retrocopy	retro_etel_14,
Felis catus	ENSFCAG00000024143	1 retrocopy	retro_fcat_1128,
Homo sapiens	ENSG00000129235	2 retrocopies	retro_hsap_132, retro_hsap_2218,
Gorilla gorilla	ENSGGOG00000003055	2 retrocopies	retro_ggor_1750, retro_ggor_230,
Macropus eugenii	ENSMEUG00000008946	1 retrocopy	retro_meug_1771,
Microcebus murinus	ENSMICG00000006620	2 retrocopies	retro_mmur_1093, retro_mmur_766,
Macaca mulatta	ENSMMUG00000003788	2 retrocopies	retro_mmul_365, retro_mmul_932,
Mustela putorius furo	ENSMPUG00000011338	2 retrocopies	retro_mputfur_518, retro_mputfur_564,
Mus musculus	ENSMUSG00000020803	3 retrocopies	retro_mmus_2817, retro_mmus_2818, retro_mmus_488,
Nomascus leucogenys	ENSNLEG00000009230	2 retrocopies	retro_nleu_2262, retro_nleu_2516,
Oryctolagus cuniculus	ENSOCUG00000016557	1 retrocopy	retro_ocun_297,
Ochotona princeps	ENSOPRG00000000509	2 retrocopies	retro_opri_575, retro_opri_8,
Procavia capensis	ENSPCAG00000003749	1 retrocopy	retro_pcap_180,
Pongo abelii	ENSPPYG00000007880	1 retrocopy	retro_pabe_485,
Pan troglodytes	ENSPTRG00000008644	2 retrocopies	retro_ptro_137, retro_ptro_1683,
Pteropus vampyrus	ENSPVAG00000002399	1 retrocopy	retro_pvam_1187,
Rattus norvegicus	ENSRNOG00000014072	1 retrocopy	retro_rnor_1700,
Sorex araneus	ENSSARG00000006501	1 retrocopy	retro_sara_20,
Ictidomys tridecemlineatus	ENSSTOG00000021986	2 retrocopies	retro_itri_197, retro_itri_574 ,
Tupaia belangeri	ENSTBEG00000000539	1 retrocopy	retro_tbel_3760,
Tarsius syrichta	ENSTSYG00000010996	2 retrocopies	retro_tsyr_1058, retro_tsyr_982,
Tursiops truncatus	ENSTTRG00000012072	1 retrocopy	retro_ttru_1252,
Vicugna pacos	ENSVPAG00000001554	1 retrocopy	retro_vpac_501,