RetrogeneDB ID: retro_itri_694

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393312.1:12291519..12292016(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL18A
• Ensembl ID: ENSSTOG00000007788
• Aliases: None
• Description: ribosomal protein L18a [Source:HGNC Symbol;Acc:10311]

Sequence

>retro_itri_694
CTTCATGAGCACAAATTAGTGGAACACTGCCTGCCCACCTCCAAATGCTCACCACCTCCCTACCAAATGCAAATTTTGTA
TCCAATTACACTGTTGCCAATTTCTGCTTCTACTATTTTGTATCTCAGCTAAAGAAGATGAGGAAGTCTACTGTCTACTG
TGGGCAGGTGTTGGAGAAGTCCCCACTATAGGAGAGAAATTTTGGCATCTGGCTGGGCTACAACTCTCACAGCAGCACCC
ACAACATGTCCTGGGAGTACTGTGACCTGACCACCACAGAAGCCATCATCCAGTGCTACTGAGATATGGGTGCATGGCAC
TTGTCCCCGGGCCACTCCATCCAGATCACAAAGGTAGAGGAGATTGTGGCCAGCAAGTGCCATCAGCCAGCAATCAAGTA
ATTCCACAACTCCAAGATCAAGTTCCCACTGTCCCATCAGGTCCTCTATCACCAGCACAAGCCACACTTCAGCACCAAGA
GGACCAATCCCTTCTTC

Alignment

ORF - retro_itri_694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.33 %
• Parental protein coverage: 96.59 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LREYKVVGRCLPTPKCHTPPLYRMRIFAP-NHVVAKSRFWYFVSQLKKMKKSSGEIVYCGQVFEKSPLRV
          L.E.K.V..CLPT.KC..PP.Y.M.I..P.N..VA...F.YFVSQLKKM.KS....VYCGQV.EKSPL..
Retrocopy LHEHKLVEHCLPTSKCSPPP-YQMQILYP<NYTVANFCFYYFVSQLKKMRKST---VYCGQVLEKSPL*E

Parental  KNFGIWLRYDSRSGTHNMYREYRDLTTAGAVTQCYRDMGARHRARAHSIQIMKVEEIAASKCRRPAVKQF
          .NFGIWL.Y.S.S.THNM..EY.DLTT..A..QCY.DMGA.H....HSIQI.KVEEI.ASKC..PA.K.F
Retrocopy RNFGIWLGYNSHSSTHNMSWEYCDLTTTEAIIQCY*DMGAWHLSPGHSIQITKVEEIVASKCHQPAIK*F

Parental  HDSKIKFPLPHRVLRRQHKPRFTTKRPNTFF
          H.SKIKFPL.H.VL..QHKP.F.TKR.N.FF
Retrocopy HNSKIKFPLSHQVLYHQHKPHFSTKRTNPFF

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_694 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_694 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 21 parental genes, and 95 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000003125	1 retrocopy	retro_acar_86,
Bos taurus	ENSBTAG00000015831	5 retrocopies	retro_btau_145, retro_btau_1586, retro_btau_842, retro_btau_917, retro_btau_922,
Canis familiaris	ENSCAFG00000015122	1 retrocopy	retro_cfam_231,
Callithrix jacchus	ENSCJAG00000014006	7 retrocopies	retro_cjac_1628, retro_cjac_2814, retro_cjac_3192, retro_cjac_3906, retro_cjac_4134, retro_cjac_441, retro_cjac_642,
Cavia porcellus	ENSCPOG00000015205	1 retrocopy	retro_cpor_1478,
Equus caballus	ENSECAG00000015258	1 retrocopy	retro_ecab_745,
Homo sapiens	ENSG00000105640	11 retrocopies	retro_hsap_1053, retro_hsap_128, retro_hsap_135, retro_hsap_1610, retro_hsap_1961, retro_hsap_2254, retro_hsap_2676, retro_hsap_2776, retro_hsap_4129, retro_hsap_4734, retro_hsap_4776,
Gorilla gorilla	ENSGGOG00000002870	8 retrocopies	retro_ggor_1215, retro_ggor_1680, retro_ggor_1868, retro_ggor_1933, retro_ggor_195, retro_ggor_227, retro_ggor_2775, retro_ggor_2940,
Macropus eugenii	ENSMEUG00000003228	2 retrocopies	retro_meug_36, retro_meug_49,
Myotis lucifugus	ENSMLUG00000006701	4 retrocopies	retro_mluc_1671, retro_mluc_1893, retro_mluc_1978, retro_mluc_2191,
Macaca mulatta	ENSMMUG00000028844	6 retrocopies	retro_mmul_1416, retro_mmul_1591, retro_mmul_2233, retro_mmul_2547, retro_mmul_292, retro_mmul_364,
Monodelphis domestica	ENSMODG00000019167	2 retrocopies	retro_mdom_349, retro_mdom_680,
Mustela putorius furo	ENSMPUG00000015786	4 retrocopies	retro_mputfur_1007, retro_mputfur_1189, retro_mputfur_1574, retro_mputfur_457,
Mus musculus	ENSMUSG00000045128	8 retrocopies	retro_mmus_1606, retro_mmus_260, retro_mmus_2910, retro_mmus_2924, retro_mmus_326, retro_mmus_346, retro_mmus_937, retro_mmus_951,
Nomascus leucogenys	ENSNLEG00000005889	7 retrocopies	retro_nleu_1087, retro_nleu_1180, retro_nleu_1940, retro_nleu_2261, retro_nleu_2605, retro_nleu_2672, retro_nleu_680,
Otolemur garnettii	ENSOGAG00000031828	4 retrocopies	retro_ogar_1016, retro_ogar_1891, retro_ogar_2226, retro_ogar_2564,
Pongo abelii	ENSPPYG00000009725	10 retrocopies	retro_pabe_1200, retro_pabe_1319, retro_pabe_1620, retro_pabe_2239, retro_pabe_2302, retro_pabe_3680, retro_pabe_3717, retro_pabe_3802, retro_pabe_482, retro_pabe_487,
Pan troglodytes	ENSPTRG00000010686	3 retrocopies	retro_ptro_1078, retro_ptro_1803, retro_ptro_27,
Rattus norvegicus	ENSRNOG00000018795	6 retrocopies	retro_rnor_108, retro_rnor_1655, retro_rnor_2279, retro_rnor_2362, retro_rnor_2821, retro_rnor_888,
Sarcophilus harrisii	ENSSHAG00000000406	3 retrocopies	retro_shar_435, retro_shar_474, retro_shar_706,
Ictidomys tridecemlineatus	ENSSTOG00000007788	1 retrocopy	retro_itri_694 ,