RetrogeneDB ID: retro_itri_179

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: AGTP01146564.1:164..416(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: BLOC1S5
• Ensembl ID: ENSSTOG00000027342
• Aliases: None
• Description: biogenesis of lysosomal organelles complex-1, subunit 5, muted [Source:HGNC Symbol;Acc:18561]

Sequence

>retro_itri_179
GAAAAACGTGGTCTTTGAGAAATGTGAGTTCTTGAAAATTGGAAGAATATGATCCATAAAACAAATGAACATACTCTTCC
CAAATGCAGAGAAATGATGCAGGAAAACTTGAACGAAGTTCTCCAGAGATTGCAAGAAGCTTATGACTCCATTTGTAGAC
TTCAGCAGAGGGAATAGGAATGAATAAAGATATATCATGACCACTTAATAGCTACTGAGAAACAGCATCAACTTCAGTGG
GAGGATTTCATG

Alignment

ORF - retro_itri_179 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.33 %
• Parental protein coverage: 68.85 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EKRGLREMRVLENLKNMIHETNEHTLPKCRETMQDNLKEVLQRLQAANDSVCRLQQREQERRKMYHDHLI
          EKRGL.EM.VLEN.KNMIH.TNEHTLPKCRE.MQ.NL.EVLQRLQ.A.DS.CRLQQRE.E..K.YHDHLI
Retrocopy EKRGL*EM*VLENWKNMIHKTNEHTLPKCREMMQENLNEVLQRLQEAYDSICRLQQRE*E*IKIYHDHLI

Parental  ATEKQHQLQWEDFM
          ATEKQHQLQWEDFM
Retrocopy ATEKQHQLQWEDFM

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_179 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_179 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017324	1 retrocopy	retro_amel_1747,
Bos taurus	ENSBTAG00000039732	2 retrocopies	retro_btau_1699, retro_btau_1747,
Monodelphis domestica	ENSMODG00000010026	1 retrocopy	retro_mdom_1483,
Oryctolagus cuniculus	ENSOCUG00000025755	2 retrocopies	retro_ocun_1051, retro_ocun_269,
Otolemur garnettii	ENSOGAG00000030827	1 retrocopy	retro_ogar_2470,
Ictidomys tridecemlineatus	ENSSTOG00000027342	3 retrocopies	retro_itri_1038, retro_itri_179 , retro_itri_1901,