RetrogeneDB ID: retro_itri_1038

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393361.1:1322777..1323045(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000027350
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1038
ATGCAGGACAACTTGAAAGAAGTTCTCCAGGGATTGCAAGCAGCTCATGACTGTAGACTCCAGCAGAGGGAACAGGAACG
AAGAAAGATGTATCATGACCACTTAATAAATAACTACTGGGAAACAGCATCAACTCCAGTGGGAGGATTTCATGAAAGAA
CAACCCTACGGTCATGCTGAGGTGGATGAAGAACACAGCAGAGCCACGGAGAGGCTTAAAGAGCAATATGCTGAGATGGA
GAAGGGCCTAGCAAAATTCTCTACTTTT

Alignment

ORF - retro_itri_1038 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.91 %
• Parental protein coverage: 73.77 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MQDNLKEVLQRLQAANDSVCRLQQR-EQERRKMYHDHL-IATEKQHQLQWEDFMKEQPRRQAEVDEEHRR
          MQDNLKEVLQ.LQAA.D..CRLQQR....R.........I.T.KQHQLQWEDFMKEQP...AEVDEEH.R
Retrocopy MQDNLKEVLQGLQAAHD--CRLQQREQERRKMYHDHLI>ITTGKQHQLQWEDFMKEQPYGHAEVDEEHSR

Parental  AMERLKEQYAEMEKGLAKFSTF
          A.ERLKEQYAEMEKGLAKFSTF
Retrocopy ATERLKEQYAEMEKGLAKFSTF

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_1038 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1038 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,