RetrogeneDB ID: retro_itri_1735

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393691.1:262202..262454(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL35
• Ensembl ID: ENSSTOG00000007901
• Aliases: None
• Description: ribosomal protein L35 [Source:HGNC Symbol;Acc:10344]

Sequence

>retro_itri_1735
AAGATGAAGGCTCAGGATCTTCTCAGCAAGGAGGAAGAGGAGCTGTTGAAATAGCTGGATGACTTGAAGGCAGAATTGTC
CCAGCTGCACATCCCCAAAGTGACAGGCAGCATTGAGTCCAAGCTCTCCAAGATGAGAGCAGTCCATAAACACATTGCTT
ATATTCTCTCCATCATTAACCAGATTCAGAAAGAAAACCTCAGGAAATTCTACAAGGGCAAGAAATTTAAACCCCAGGAT
CTACACCAAAAA

Alignment

ORF - retro_itri_1735 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 68.29 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KIKARDLRGKKKEELLKQLDDLKVELSQLRVAKVTGGAASKLSKIRVVRKSIARVLTVINQTQKENLRKF
          K.KA.DL..K..EELLK.LDDLK.ELSQL...KVTG...SKLSK.R.V.K.IA..L..INQ.QKENLRKF
Retrocopy KMKAQDLLSKEEEELLK*LDDLKAELSQLHIPKVTGSIESKLSKMRAVHKHIAYILSIINQIQKENLRKF

Parental  YKGKKYKPLDLRPK
          YKGKK.KP.DL..K
Retrocopy YKGKKFKPQDLHQK

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_1735 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1735 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 20 parental genes, and 86 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016537	12 retrocopies	retro_amel_1010, retro_amel_1180, retro_amel_1341, retro_amel_1686, retro_amel_1746, retro_amel_1844, retro_amel_1887, retro_amel_351, retro_amel_584, retro_amel_819, retro_amel_893, retro_amel_94,
Bos taurus	ENSBTAG00000003205	3 retrocopies	retro_btau_1060, retro_btau_1340, retro_btau_185,
Cavia porcellus	ENSCPOG00000022811	1 retrocopy	retro_cpor_414,
Equus caballus	ENSECAG00000009389	3 retrocopies	retro_ecab_1083, retro_ecab_115, retro_ecab_813,
Erinaceus europaeus	ENSEEUG00000012696	8 retrocopies	retro_eeur_144, retro_eeur_217, retro_eeur_225, retro_eeur_251, retro_eeur_319, retro_eeur_487, retro_eeur_533, retro_eeur_56,
Felis catus	ENSFCAG00000030388	5 retrocopies	retro_fcat_1129, retro_fcat_1790, retro_fcat_1954, retro_fcat_397, retro_fcat_782,
Gorilla gorilla	ENSGGOG00000004111	3 retrocopies	retro_ggor_2581, retro_ggor_351, retro_ggor_966,
Loxodonta africana	ENSLAFG00000010031	3 retrocopies	retro_lafr_128, retro_lafr_300, retro_lafr_642,
Myotis lucifugus	ENSMLUG00000029323	3 retrocopies	retro_mluc_1495, retro_mluc_2392, retro_mluc_969,
Macaca mulatta	ENSMMUG00000005260	5 retrocopies	retro_mmul_1304, retro_mmul_156, retro_mmul_1623, retro_mmul_1912, retro_mmul_265,
Monodelphis domestica	ENSMODG00000019753	1 retrocopy	retro_mdom_1039,
Mustela putorius furo	ENSMPUG00000013950	5 retrocopies	retro_mputfur_1136, retro_mputfur_1348, retro_mputfur_1478, retro_mputfur_1484, retro_mputfur_425,
Mus musculus	ENSMUSG00000062997	1 retrocopy	retro_mmus_236,
Ornithorhynchus anatinus	ENSOANG00000011612	1 retrocopy	retro_oana_56,
Oryctolagus cuniculus	ENSOCUG00000002996	4 retrocopies	retro_ocun_200, retro_ocun_238, retro_ocun_451, retro_ocun_791,
Pongo abelii	ENSPPYG00000019603	7 retrocopies	retro_pabe_1026, retro_pabe_165, retro_pabe_1718, retro_pabe_2948, retro_pabe_3064, retro_pabe_3303, retro_pabe_3304,
Rattus norvegicus	ENSRNOG00000014272	14 retrocopies	retro_rnor_1254, retro_rnor_126, retro_rnor_147, retro_rnor_1473, retro_rnor_1509, retro_rnor_1768, retro_rnor_1957, retro_rnor_205, retro_rnor_2183, retro_rnor_233, retro_rnor_2618, retro_rnor_2681, retro_rnor_2719, retro_rnor_451,
Sarcophilus harrisii	ENSSHAG00000004756	1 retrocopy	retro_shar_775,
Sus scrofa	ENSSSCG00000005595	5 retrocopies	retro_sscr_1168, retro_sscr_214, retro_sscr_553, retro_sscr_679, retro_sscr_905,
Ictidomys tridecemlineatus	ENSSTOG00000007901	1 retrocopy	retro_itri_1735 ,