RetrogeneDB ID: retro_itri_586

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393303.1:11160164..11160995(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSTOG00000003865
• Aliases: None
• Description: None

Sequence

>retro_itri_586
ATGGAGAACAATGAAAACTCAGTGGATTCAAAATCCATTAAAAATTTGAACCAAAGACCATACATGGAAACAAATCAATG
GACTCTGGAATATCCTTGGACAATCGTTACAAAATGGATTATCCTGAAATGGGTTTATGTTTAATCATTAATAATAAGAA
CTTTCATAAAAGCACTGGAATGGCCTCTCGGTCTGGTACAGATGTAGATGCAGCAAACCTCCGAGAAATATTCATGAACT
TGAAATATGAAGTCAGGAATAAAAATGACCTTACACGTGAAGAAATTGTGGAGTTAATGCACAATGTTTCTAAAGAAGAT
CATAGCAAAAGGAGCAGCTTTATTTGTGTAATTCTAAGCCATGGTGATGAAGGAATAATATTTGGAACAAATGGACCTGT
TGACCTGAAAATATTAACAAGTTTCTTCAGAGGAGATTATTGCAGAAGTCTTAATTGGAAAACCCAAACTTTTCATTATT
CAGGCCTGCCGGGGTACAGAACTAGACTGTGGCATTGAGACAGACAGTGGCATTGATGATGACATAGCATGCCACAAAAT
ACCAGTAGAGGCCGACTTCTTATATGCATATTCTACAGCACCAGGTTACTATTCCTGGCGAAATTCCAAGGATGGATCCT
AGTTCATCCAGTCACTGTGTGCTCTGCTGAAACAATACGCTCATAAGCTTGAGTTTATGCATATTCTCACTCGGGTAAAC
CGGAAGGTAGCAACAGAATTTGAGTTCTTTTCTCTTGACTCCACTTTTCATGCAAAGAAACAGATTCCATGTATTGTGTC
CATGCTCACAAAAGAACTGTATTTTTATCCC

Alignment

ORF - retro_itri_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MENNENSVDSKSIKN-FEQKTIHGSKSMDSGISLDNRYKMDYPEMGLCLIINNKNFHKSTGMAYRSGTDV
          MENNENSVDSKSIKN.FE.KTIHG.KSMDSGISLDNRYKMDYPEMGLCLIINNKNFHKSTGMA.RSGTDV
Retrocopy MENNENSVDSKSIKN<FEPKTIHGNKSMDSGISLDNRYKMDYPEMGLCLIINNKNFHKSTGMASRSGTDV

Parental  DAANLREIFMNLKYEVRNKNDLTREEIVELLHNVSKEDHSKRSSFVCIILSHGDEGIIFGTNGPVDLKKL
          DAANLREIFMNLKYEVRNKNDLTREEIVEL.HNVSKEDHSKRSSF.C.ILSHGDEGIIFGTNGPVDLK.L
Retrocopy DAANLREIFMNLKYEVRNKNDLTREEIVELMHNVSKEDHSKRSSFICVILSHGDEGIIFGTNGPVDLKIL

Parental  TSFFRGDYCRSLT-GKPKLFIIQACRGTELDCGIETDSGIDDDMACHKIPVEADFLYAYSTAPGYYSWRN
          TSFFRGDYCRSL..GKPKLFIIQACRGTELDCGIETDSGIDDD.ACHKIPVEADFLYAYSTAPGYYSWRN
Retrocopy TSFFRGDYCRSLN>GKPKLFIIQACRGTELDCGIETDSGIDDDIACHKIPVEADFLYAYSTAPGYYSWRN

Parental  SKDGSWFIQSLCALLKQYAHKLEFMHILTRVNRKVATEFESFSLDSTFHAKKQIPCIVSMLTKELYFYP
          SKDGS.FIQSLCALLKQYAHKLEFMHILTRVNRKVATEFE.FSLDSTFHAKKQIPCIVSMLTKELYFYP
Retrocopy SKDGS*FIQSLCALLKQYAHKLEFMHILTRVNRKVATEFEFFSLDSTFHAKKQIPCIVSMLTKELYFYP

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_586 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_586 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005740	2 retrocopies	retro_cjac_2678, retro_cjac_3011,
Cavia porcellus	ENSCPOG00000012511	2 retrocopies	retro_cpor_1203, retro_cpor_1450,
Dasypus novemcinctus	ENSDNOG00000013931	1 retrocopy	retro_dnov_1013,
Dipodomys ordii	ENSDORG00000002554	2 retrocopies	retro_dord_178, retro_dord_620,
Homo sapiens	ENSG00000164305	1 retrocopy	retro_hsap_406,
Gorilla gorilla	ENSGGOG00000025155	1 retrocopy	retro_ggor_402,
Microcebus murinus	ENSMICG00000004809	2 retrocopies	retro_mmur_1389, retro_mmur_691,
Macaca mulatta	ENSMMUG00000012053	1 retrocopy	retro_mmul_114,
Nomascus leucogenys	ENSNLEG00000010895	1 retrocopy	retro_nleu_1005,
Otolemur garnettii	ENSOGAG00000005985	2 retrocopies	retro_ogar_1756, retro_ogar_3263,
Pongo abelii	ENSPPYG00000015236	1 retrocopy	retro_pabe_312,
Pan troglodytes	ENSPTRG00000016640	1 retrocopy	retro_ptro_310,
Rattus norvegicus	ENSRNOG00000010475	1 retrocopy	retro_rnor_2747,
Sarcophilus harrisii	ENSSHAG00000009178	1 retrocopy	retro_shar_404,
Ictidomys tridecemlineatus	ENSSTOG00000003865	2 retrocopies	retro_itri_172, retro_itri_586 ,