RetrogeneDB ID: retro_itri_923

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393344.1:8886940..8887820(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIMP2
• Ensembl ID: ENSSTOG00000029156
• Aliases: None
• Description: aminoacyl tRNA synthetase complex-interacting multifunctional protein 2 [Source:HGNC Symbol;Acc:20609]

Sequence

>retro_itri_923
ATGCCGATGAACCAGGTAAAGCCCTATCACGGGGGGCGGCACACCGCTGCGTGTAGAGCTTCCCACCTGCGTGTACCGGC
TCCCCAACATGCACTGTAGGACCGGCAGCCCCGCGCTCGAGGCCGGCCACGTGCAGGAAGCATCTGACCCCTCTCTGCAA
GCTCTTGAGTCCCGCCAAGATGATATTTTTAAAACGTTTGTATGAGTTGAAAGCTGCAGTCGATGGTCTCTCCAAGATGA
TTCACACACCAGATGCAGACATGGATGTGACAAACATCATGCAAGCTGATGAGCCCACTTCTTTCACAACCAATGCATTC
GATTTGCATTCAGTGCTTGGAAAGGACTATGGAGCGCTGAAAGACAACGTGATCAACGCAAACCCTGCCTCCCCTCCTCT
CTGCCTGCTCGTGCTGCATAGGTAGCTCTGTGAGAGCTACAGGGTGCTATCCACTGTGCACACACATTCATCAGTGAAGA
GTGTGCCTGAGACCCTTCTCAAGTGCTTTGGGGAACAGACTAGGAAAGAGCCCCGTCATGAGTATCAGCTGGGCTTCACT
TTAATTTGGAAGAATGTGCCCAAGACTCAAATGAAGTTTAGTGTCCAGACAATGTGCTCCATTGAAGGAGAAGGGAACAT
TGCACTTTTCTTGTTCTCTCTGTTTGGCCAGAAGCATAATGCCATCAACTCAACCCTCATAGATAGCAGGGTAGATATCG
ATATTTTTCAGCTAAAAGAGGGGAGCAGTAAAGAAAAGGTAGCTGTTTTCGCTCCATGAACTCTGCTCTGGGGAGGAGCC
CGTGGCTGGTTGGGAACGAGCTCACCATGGCAGATGTTGCGCTGTGGTGTGTGCGCCAGCAGACAGGAGGCTGCAGTGCC

Alignment

ORF - retro_itri_923 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.2 %
• Parental protein coverage: 91.56 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MPMYQVKPYHGG-GAPLRVELPTCMYRLPNVHCRTGSPAPEAGHXXEAPDPSLQALESRQDDI-LKRLYE
          MPM.QVKPYHGG.G.PLRVELPTC.YRLPN.HCRTGSPA.EAGH..EA.DPSLQALESRQDDI.LKRLYE
Retrocopy MPMNQVKPYHGG>GTPLRVELPTCVYRLPNMHCRTGSPALEAGHVQEASDPSLQALESRQDDI>LKRLYE

Parental  LKAAVDGLSKMIHTPDADMDVTNIMQADEPTTLTTNALDLNSVLGKDYGALKDIVINANPASPPLCLLVL
          LKAAVDGLSKMIHTPDADMDVTNIMQADEPT..TTNA.DL.SVLGKDYGALKD.VINANPASPPLCLLVL
Retrocopy LKAAVDGLSKMIHTPDADMDVTNIMQADEPTSFTTNAFDLHSVLGKDYGALKDNVINANPASPPLCLLVL

Parental  HRLLCESYRVLSTVHTHSSVKSVPENLLKCFGEQTRKQPRHEYQLGFTLIWKNVPKTQMKFSVQTMCPIE
          HR.LCESYRVLSTVHTHSSVKSVPE.LLKCFGEQTRK.PRHEYQLGFTLIWKNVPKTQMKFSVQTMC.IE
Retrocopy HR*LCESYRVLSTVHTHSSVKSVPETLLKCFGEQTRKEPRHEYQLGFTLIWKNVPKTQMKFSVQTMCSIE

Parental  GEGNIARFLFSLFGQKHNAINSTLIDSWVDIAIFQLKEGSSKEKAAV-FRSMNSALGKSPWLVGNELTVA
          GEGNIA.FLFSLFGQKHNAINSTLIDS.VDI.IFQLKEGSSKEK.AV.FRSMNSALG.SPWLVGNELT.A
Retrocopy GEGNIALFLFSLFGQKHNAINSTLIDSRVDIDIFQLKEGSSKEKVAV<FRSMNSALGRSPWLVGNELTMA

Parental  DVVLWSVLQQTGGCSA
          DV.LW.V.QQTGGCSA
Retrocopy DVALWCVRQQTGGCSA

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_923 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_923 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Pteropus vampyrus	ENSPVAG00000016092	1 retrocopy	retro_pvam_27,
Rattus norvegicus	ENSRNOG00000001044	1 retrocopy	retro_rnor_2324,
Ictidomys tridecemlineatus	ENSSTOG00000029156	1 retrocopy	retro_itri_923 ,