RetrogeneDB ID: retro_itri_628

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393308.1:808087..808686(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EMC10
• Ensembl ID: ENSSTOG00000011644
• Aliases: None
• Description: ER membrane protein complex subunit 10 [Source:HGNC Symbol;Acc:27609]

Sequence

>retro_itri_628
GATGACAGTGCCCACTTTCGGAAACGGGGCTCACTACTCTAGAATCAGCAGGATGGCACCTTATCCTTATCACAGCAGCA
GCTCAGCGAGGAGGAGCGGGACCGACTTCGGGATGTGGCAGCCCTCAAAGGCCTGTACCGGGTGCGGGTCCCGAGGCAGC
CAGGGGTCCCTGATGGGTCAGAAGCTGGCGGCTATGTCTCTTCCTTTGTCCCTGCGTGCTCCCTGGTGGAGTCACATCTC
TCAGACCAGCTGACCCTGCACGTGGATGTGGCTGGCAATGTGGTGGGTGTGTCAGTGGTGACACACCCTGGGGGGGTGCC
AAGGCCATGAGGTGGAGGATATGGACCTGGAGCTGTTTAATACATCTGTGCAGCTGCGGCCCCCAGGCACAGCCCCAGGT
CCAGAAACAGCAGCCTTCATTGAGCGCCTAGAGATGGAGCAGGCCCAGAAGGCCAAGACCCCCCAGGAGCAGAAGTCCTT
TTTTGCCAAATATTGGATGTACATCATTCCTGTTGTCCTGTTCCTCATGATATCAGGAGCACCAGACGACGGGGAGCCAG
AGTGGCGGTGGGAGTGGGGGTGGCAGAGGGGGTAGTGGC

Alignment

ORF - retro_itri_628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.53 %
• Parental protein coverage: 99.5 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DDSAHFRKRGSLLWNQQDGTLSLSQRQLSEEERGRLRDVAALNGLYRVRVPRQPGVPDGSEAGGYVSSFV
          DDSAHFRKRGSLL.NQQDGTLSLSQ.QLSEEER.RLRDVAAL.GLYRVRVPRQPGVPDGSEAGGYVSSFV
Retrocopy DDSAHFRKRGSLL*NQQDGTLSLSQQQLSEEERDRLRDVAALKGLYRVRVPRQPGVPDGSEAGGYVSSFV

Parental  PACSLVESHLSDQLTLHVDVAGNVVGVSVVTHPGG-CRGHEVEDVDLELFNTSVQLRPPGTAPGPETAAF
          PACSLVESHLSDQLTLHVDVAGNVVGVSVVTHPGG.C.GHEVED.DLELFNTSVQLRPPGTAPGPETAAF
Retrocopy PACSLVESHLSDQLTLHVDVAGNVVGVSVVTHPGG>CQGHEVEDMDLELFNTSVQLRPPGTAPGPETAAF

Parental  IERLEMEQAQKAKNPQEQKSFFAKYWMYIIPVVLFLMMSGAPD-AGGQSGGGSGGGSGGSG
          IERLEMEQAQKAK.PQEQKSFFAKYWMYIIPVVLFLM.SGAPD..G.QSGGGSGGG.GGSG
Retrocopy IERLEMEQAQKAKTPQEQKSFFAKYWMYIIPVVLFLMISGAPD>TGSQSGGGSGGGRGGSG

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_628 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_628 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Mustela putorius furo	ENSMPUG00000001776	1 retrocopy	retro_mputfur_175,
Ictidomys tridecemlineatus	ENSSTOG00000011644	1 retrocopy	retro_itri_628 ,