RetrogeneDB ID: retro_itri_546

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393300.1:12657495..12658629(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025444
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: STT3A
• Ensembl ID: ENSSTOG00000020526
• Aliases: None
• Description: STT3A, subunit of the oligosaccharyltransferase complex (catalytic) [Source:HGNC Symbol;Acc:6172]

Sequence

>retro_itri_546
ATGACTAAGCTTGGATTTTGGCGACTGTCCCATGAGAAGCAGGACACTCTTCTGAAGCTTCTCATTCTATCAATGGCTGC
TGTGTTATCTTTCTCCACTTGTCTCTTTGCTGTCCTGAGATTCGAAAGTGTTATCCATGAGTTCGATCCGTATTTTAATT
ATCGGACTACCAGGTTCCTGGCTGAGGAGGGATTTTATAAATTCCATAACTGGTTTGATGACTGGGCCTGGTACCCTTTG
GGACGAATCATTGGAGGAACAAATTATCCAGGCTTAATGATCACCTCTGCTGCAATCTACTATGTTCTCCATTTTTTTCA
CATCACCATCGACATTCGGAATGTCTGTGTGTTCCTGGCCCCACTCTTCTCTTCCTTCACCACCATCGTCACGTACCATC
TTACCAAAGAGCTCAAGGATGCAGGGGCTGGACTTCTTGCTGCTGCCATGATTGCTGTAGTTCCTGGATATATCTCCCGA
TCTGTGGCTGGTTCCTATGATAATGAAGGGATTGCCATCTTTTGCATGCTCCTCACCTACTACATGTGGATCAAGGCAGT
GAAGACTGGTTCTATCTATTGGACAGCCAAGTGTGCTTTTGCTTATTTCTACATGGTTTCCTCATGGGGAGGTTATGTGT
TCCTGATCAACTTGATTCCTCTTCATGTTCTGGTGCTGATGCTCACAGGCCGTTTCTCCCACCGGATTTATGTGGCCTAT
TTCACAGTTTACTGCCTGGGCACCATTCTTTCCATGCAGATCTCCTTTGTGGGTTTCCAGCCAGTCCTTTCATCAGAGCA
CATGGCAGCCTTTGGAGTCTTTGGTCTTTGCCAGATCCATGCCTTTGTGGATTACCTGCGCAGCAAATTAAATCCACAGC
AATTTGAAGTTCTTTTCCGTAGTGTCATATCCCTGGTAGGCTTTGTCCTACTCACTGTGGGAGCTCTCCTCATGCTGACA
GGAAAAATATCTCCATGGACGGGGTGTTTCTACTCACTGCTGGATCCTTCTTATGCTAAGAACAACATCCCCATCATTGC
TTCTGTGTCCGAGCATCAGCCCACAACCTGGTCTTCCTACTATTTTGATCTGCAGCTCCTCGTTTTGGTCTCTATTACTG
CTTTAGCAACCTGT

Alignment

ORF - retro_itri_546 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.99 %
• Parental protein coverage: 53.68 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTKLGFLRLSYEKQDTLLKLLILSMAAVLSFSTRLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN
          MTKLGF.RLS.EKQDTLLKLLILSMAAVLSFST.LFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN
Retrocopy MTKLGFWRLSHEKQDTLLKLLILSMAAVLSFSTCLFAVLRFESVIHEFDPYFNYRTTRFLAEEGFYKFHN

Parental  WFDDRAWYPLGRIIGGTIYPGLMITSAAIYHVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD
          WFDD.AWYPLGRIIGGT.YPGLMITSAAIY.VLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD
Retrocopy WFDDWAWYPLGRIIGGTNYPGLMITSAAIYYVLHFFHITIDIRNVCVFLAPLFSSFTTIVTYHLTKELKD

Parental  AGAGLLAAAMIAVVPGYISRSVAGSYDNEAGIAIFCMLLTYYMWIKAVKTGSIYWAAKCALAYFYMVSSW
          AGAGLLAAAMIAVVPGYISRSVAGSYDNE.GIAIFCMLLTYYMWIKAVKTGSIYW.AKCA.AYFYMVSSW
Retrocopy AGAGLLAAAMIAVVPGYISRSVAGSYDNE-GIAIFCMLLTYYMWIKAVKTGSIYWTAKCAFAYFYMVSSW

Parental  GGYVFLINLIPLHVLVLMLTGRFSHRIYVAYCTVYCLGTILSMQISFVGFQPVLSSEHMAAFGVFGLCQI
          GGYVFLINLIPLHVLVLMLTGRFSHRIYVAY.TVYCLGTILSMQISFVGFQPVLSSEHMAAFGVFGLCQI
Retrocopy GGYVFLINLIPLHVLVLMLTGRFSHRIYVAYFTVYCLGTILSMQISFVGFQPVLSSEHMAAFGVFGLCQI

Parental  HAFVDYLRSKLNPQQFEVLFRSVISLVGFVLLTVGALLMLTGKISPWTGRFYSLLDPSYAKNNIPIIASV
          HAFVDYLRSKLNPQQFEVLFRSVISLVGFVLLTVGALLMLTGKISPWTG.FYSLLDPSYAKNNIPIIASV
Retrocopy HAFVDYLRSKLNPQQFEVLFRSVISLVGFVLLTVGALLMLTGKISPWTGCFYSLLDPSYAKNNIPIIASV

Parental  SEHQPTTWSSYYFDLQLLVFMFPVGLYYC
          SEHQPTTWSSYYFDLQLLV......L..C
Retrocopy SEHQPTTWSSYYFDLQLLVLVSITALATC

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_546 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_546 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
Oryctolagus cuniculus	ENSOCUG00000014677	1 retrocopy	retro_ocun_684,
Ictidomys tridecemlineatus	ENSSTOG00000020526	1 retrocopy	retro_itri_546 ,