RetrogeneDB ID: retro_itri_432

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393291.1:7174233..7174557(+)
• Located in intron of: ENSSTOG00000007352

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRP14
• Ensembl ID: ENSSTOG00000015627
• Aliases: None
• Description: signal recognition particle 14kDa (homologous Alu RNA binding protein) [Source:HGNC Symbol;Acc:11299]

Sequence

>retro_itri_432
ATGGTGCTGCTGGAGAGCAAGCAGTTCCCGATGGAGCGGACCAGGCTCTTCCAGAAGTGTGGGTGGTTGGGCATCGAGTA
CACCCGCCTTGAAGCGGTGTGATGGTCAAACCGAACCCGCACCCAGGAAGGGTTCTGTGGAGGGCGTTGAGCCCTCAGAC
AACAAGTGTCTGTCGAGAGCAACAGACGGGAAAAAGAGGATCAGCACAGGTCGAGCTCCAAAGACGTGAAGAAGCTTCAG
GTGGCTTATTCAAACCTGCTCAGAGCTCACATGGAGGGGGCCGAGGACCAGAGACAGAGCAAGAGAAAGAAGAGCAAAGC
GGCT

Alignment

ORF - retro_itri_432 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.57 %
• Parental protein coverage: 99.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MVLLESEQFLTELTRLFQKCRLSGSVYI-TLKKYDGRTKPTPRKGSVEGVEPSDNKCLLRATDGKKKIST
          MVLLES.QF..E.TRLFQKC...G..Y...LK..DG.T.P.PRKGSVEGVEPSDNKCL.RATDGKK.IST
Retrocopy MVLLESKQFPMERTRLFQKCGWLGIEYT>ALKRCDGQTEPAPRKGSVEGVEPSDNKCLSRATDGKKRIST

Parental  -VVSSKEVNKFQMAYSNLLRANMDGLKKRDKKSKSKKSKAA
          ...SSK.V.K.Q.AYSNLLRA.M.G.......SK.KKSKAA
Retrocopy <RSSSKDVKKLQVAYSNLLRAHMEGAEDQ-RQSKRKKSKAA

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_432 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_432 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 16 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000029889	2 retrocopies	retro_cfam_210, retro_cfam_40,
Callithrix jacchus	ENSCJAG00000020912	3 retrocopies	retro_cjac_1642, retro_cjac_171, retro_cjac_3057,
Equus caballus	ENSECAG00000000319	1 retrocopy	retro_ecab_817,
Echinops telfairi	ENSETEG00000011870	1 retrocopy	retro_etel_1094,
Felis catus	ENSFCAG00000030207	2 retrocopies	retro_fcat_1425, retro_fcat_1684,
Gorilla gorilla	ENSGGOG00000009921	1 retrocopy	retro_ggor_665,
Microcebus murinus	ENSMICG00000007637	1 retrocopy	retro_mmur_487,
Macaca mulatta	ENSMMUG00000016061	4 retrocopies	retro_mmul_1228, retro_mmul_1740, retro_mmul_573, retro_mmul_780,
Monodelphis domestica	ENSMODG00000029204	1 retrocopy	retro_mdom_1806,
Mustela putorius furo	ENSMPUG00000008324	1 retrocopy	retro_mputfur_376,
Otolemur garnettii	ENSOGAG00000029070	2 retrocopies	retro_ogar_2839, retro_ogar_40,
Pongo abelii	ENSPPYG00000006342	3 retrocopies	retro_pabe_1534, retro_pabe_262, retro_pabe_811,
Pteropus vampyrus	ENSPVAG00000002186	2 retrocopies	retro_pvam_152, retro_pvam_323,
Ictidomys tridecemlineatus	ENSSTOG00000015627	9 retrocopies	retro_itri_1334, retro_itri_1501, retro_itri_1633, retro_itri_382, retro_itri_432 , retro_itri_707, retro_itri_710, retro_itri_799, retro_itri_824,
Tursiops truncatus	ENSTTRG00000000036	5 retrocopies	retro_ttru_1185, retro_ttru_1288, retro_ttru_594, retro_ttru_74, retro_ttru_782,
Vicugna pacos	ENSVPAG00000010282	1 retrocopy	retro_vpac_20,