RetrogeneDB ID: retro_itri_1571

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393550.1:226681..226988(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: OSTC
• Ensembl ID: ENSSTOG00000021644
• Aliases: None
• Description: oligosaccharyltransferase complex subunit (non-catalytic) [Source:HGNC Symbol;Acc:24448]

Sequence

>retro_itri_1571
CCACATGCAACGGTACTGTACACTCTGGTGAGGGGTGTCTTACTTCCTCATCACCAGAGGAATAATTTATGATATTTTAT
TGTTGAACCTTCAAGCATTGGCTCTATGACTGATAAATATGGGCCTCAGAGGTCAGTAGCTTTCTGGACCTACAGAGTAA
ATGGACAATATAACCCGGAAGGACTCACATTCAGCTTCCTGCTTACAGTAGGAGGTTTAAGTTTCACAATCCTGGACCCA
TCTAATAAAAAAATTCCAAAACTCAACAGATTTTTTTCTCCTATTAGTTGGATTCATTTACGCTCTA

Alignment

ORF - retro_itri_1571 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.32 %
• Parental protein coverage: 68.46 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  PSAMTVYALVV-VSYFLITGGIIYDVI-VEPPS-VGSMTDEHGHQRPVAFLAYRVNGQYIMEGLASSFLF
          P.A...Y.LV..VSYFLIT.GIIYD......PS..GSMTD..G.QR.VAF..YRVNGQY..EGL..SFL.
Retrocopy PHATVLYTLVR>VSYFLITRGIIYDIL<IVEPSSIGSMTDKYGPQRSVAFWTYRVNGQYNPEGLTFSFLL

Parental  TMGGLGFIILDRSNAPNIPKLNR-FLLLFIGFVCVL
          T.GGL.F.ILD.SN...IPKLNR.F.LL..GF...L
Retrocopy TVGGLSFTILDPSN-KKIPKLNR>FFLLLVGFIYAL

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_1571 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1571 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 17 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001753	2 retrocopies	retro_amel_1110, retro_amel_165,
Canis familiaris	ENSCAFG00000011286	12 retrocopies	retro_cfam_1129, retro_cfam_1206, retro_cfam_1459, retro_cfam_1462, retro_cfam_1575, retro_cfam_1851, retro_cfam_1910, retro_cfam_1948, retro_cfam_2003, retro_cfam_263, retro_cfam_296, retro_cfam_814,
Callithrix jacchus	ENSCJAG00000016002	3 retrocopies	retro_cjac_121, retro_cjac_2981, retro_cjac_324,
Cavia porcellus	ENSCPOG00000024467	1 retrocopy	retro_cpor_659,
Echinops telfairi	ENSETEG00000003717	4 retrocopies	retro_etel_1564, retro_etel_492, retro_etel_878, retro_etel_970,
Gorilla gorilla	ENSGGOG00000026873	6 retrocopies	retro_ggor_1457, retro_ggor_2060, retro_ggor_215, retro_ggor_2427, retro_ggor_370, retro_ggor_385,
Monodelphis domestica	ENSMODG00000020599	1 retrocopy	retro_mdom_428,
Mustela putorius furo	ENSMPUG00000008869	1 retrocopy	retro_mputfur_1451,
Mus musculus	ENSMUSG00000041084	1 retrocopy	retro_mmus_648,
Nomascus leucogenys	ENSNLEG00000012929	11 retrocopies	retro_nleu_1372, retro_nleu_1436, retro_nleu_2026, retro_nleu_2265, retro_nleu_2274, retro_nleu_2665, retro_nleu_2796, retro_nleu_2826, retro_nleu_297, retro_nleu_474, retro_nleu_923,
Oryctolagus cuniculus	ENSOCUG00000011056	2 retrocopies	retro_ocun_1318, retro_ocun_7,
Otolemur garnettii	ENSOGAG00000033684	1 retrocopy	retro_ogar_578,
Pteropus vampyrus	ENSPVAG00000005915	1 retrocopy	retro_pvam_924,
Rattus norvegicus	ENSRNOG00000023322	1 retrocopy	retro_rnor_2297,
Sus scrofa	ENSSSCG00000009145	1 retrocopy	retro_sscr_503,
Ictidomys tridecemlineatus	ENSSTOG00000021644	6 retrocopies	retro_itri_1211, retro_itri_1386, retro_itri_15, retro_itri_1571 , retro_itri_789, retro_itri_863,
Tarsius syrichta	ENSTSYG00000000724	2 retrocopies	retro_tsyr_1193, retro_tsyr_921,