RetrogeneDB ID: retro_itri_940

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393346.1:2550318..2551504(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AARSD1
• Ensembl ID: ENSSTOG00000000481
• Aliases: None
• Description: alanyl-tRNA synthetase domain containing 1 [Source:HGNC Symbol;Acc:28417]

Sequence

>retro_itri_940
ATGGTCTCCTGTTAGCCAGCTGAGATGCAGACCCATGGGAGCAATGGCAAGAAAGAAGGGCTGAGCGGTTTCCATGTGGT
GTTGGAAGACATGCTACTTTTCCCTAAGGGCAGGGGACAACCTAATGACCATGGCACAATCAATGACATCTCTGTACTGA
GAGTGACCTGCCGGGGAGCCCAGGCTGATCATTTCACAGGGACATCTCTGGCCCCTGGGAGCCAGTTTCAGGTCCAGGTT
GACTGGGAGCGGAGGTTTGATCACATGCAGTAGCATTCAGGGCAGCATCTCATCACAGCAGTGGCTGATAGTCTATTTGG
GTTGAAGACAACATCATGGGAGTTAGGGAGACTCTGGAGTGTAATTGAGCTGGACAGCCCCTTTGTGACTGCAGAACAAG
TAGCTACCATTGAGCAGAGTGTCAATGAAAAAATCAGAGATCAGTTGCCTGTGAGTGTTCAAGAACTGAGCCTGGATGAT
CCTGAGGTGGAGAAGGTGAGAGGCTCGGGATTACCAGATGATCATGCTGGACCCATTCAAGATGTTACCATTGAGGGTGT
TGATTCTAACAGGTGCTGTGGGACTCATGTAAACAATCTCAGTTACCTTCAGATCATAAAGATTCTGGTTACTGAGAAGG
GGAAAAAGAATAAAACCAACCTGATATTTCTGGCTGGGAACCAGGTGCTCAAGTGAATGGAGAGAAGTCACGGAACTGAA
AATGCACTGACCACTCTGCTTAAGTGTGGAACATAAGATCATGTGGAAGCAGTGAAAAAGCTCCAGAACTACTCCAAATT
CTTGCAGAAAAATAACCTGAATCTGCTCAGAGACCTGGCTGTGCACATTGTTCACTGTCTCAGGAATAGCCCAGACTAGG
GAGGTGCGGTCATACAATACAGGAAGGAGGGAGATTCTGAGTTCATGAATATCATTGCCAGTGAAATTGGGTCAGAGGAG
ACCCTCCTCTTCCTAACTGTGGGAGACGAGAAAGGTGCTGGGCTCTTCTTACTGGCAGGGCCAGCGGAGGCTGTGGAAAC
CTGAGGTCCAGGGTGGCTGAGGTCCTGGAAGGCAAAAAGAGCAGGGAAGAAAGGCCGCTTCCAGGGCAAGGCCACCAAGA
TGAGCCAGCGGGGCAGAGGTGCAGGTACTTCTATAAGACTATGTCAGCACGCAGAGCACTGAGGAG

Alignment

ORF - retro_itri_940 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.93 %
• Parental protein coverage: 99. %
• Number of stop codons detected: 7
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VVSCQPAELQTDGSNGKKEALSGFHVVLEDTLLFPEGGGQPDDRGTINDISVLRVTRRGAQADHFTQTPL
          .VSC.PAE.QT.GSNGKKE.LSGFHVVLED.LLFP.G.GQP.D.GTINDISVLRVT.RGAQADHFT.T.L
Retrocopy MVSC*PAEMQTHGSNGKKEGLSGFHVVLEDMLLFPKGRGQPNDHGTINDISVLRVTCRGAQADHFTGTSL

Parental  APGSQVQVQVDWERRFDHMQQHSGQHLITAVADNLFGLKTTSWELGRHRSVIELDSPSVTAEQVATIEQC
          APGSQ.QVQVDWERRFDHMQ.HSGQHLITAVAD.LFGLKTTSWELGR..SVIELDSP.VTAEQVATIEQ.
Retrocopy APGSQFQVQVDWERRFDHMQ*HSGQHLITAVADSLFGLKTTSWELGRLWSVIELDSPFVTAEQVATIEQS

Parental  VNEKIRDRLPVSVQELSLDDPEVEKVRGRGLPDDHAGPIRVVTIEGVDSNMCCGTHVNNLSDLQVIKILG
          VNEKIRD.LPVSVQELSLDDPEVEKVRG.GLPDDHAGPI..VTIEGVDSN.CCGTHVNNLS.LQ.IKIL.
Retrocopy VNEKIRDQLPVSVQELSLDDPEVEKVRGSGLPDDHAGPIQDVTIEGVDSNRCCGTHVNNLSYLQIIKILV

Parental  TEKGKKNKTNLIFLAGNRVLKWMERSHGTEKALTTLLKCGAEDHVEAVKKLQNSSKLLQKNNLNLLRDLA
          TEKGKKNKTNLIFLAGN.VLK.MERSHGTE.ALTTLLKCG..DHVEAVKKLQN.SK.LQKNNLNLLRDLA
Retrocopy TEKGKKNKTNLIFLAGNQVLK*MERSHGTENALTTLLKCGT*DHVEAVKKLQNYSKFLQKNNLNLLRDLA

Parental  VHIAHCLRNSPDWGGVVVLHRKEGDSEFMNIIANEIGSEETLLFLTVGDEKGAGLFLLAGPAEAVETLGP
          VHI.HCLRNSPD.GG.V...RKEGDSEFMNIIA.EIGSEETLLFLTVGDEKGAGLFLLAGPAEAVET.GP
Retrocopy VHIVHCLRNSPD*GGAVIQYRKEGDSEFMNIIASEIGSEETLLFLTVGDEKGAGLFLLAGPAEAVET*GP

Parental  -RVAEVLEG-KGAGKKGRFQGKATKMNRR-AEVQALLQDYVSTQSAEE
          .RVAEVLEG.K.AGKKGRFQGKATKM..R.AEVQ.LL.DYVSTQS.EE
Retrocopy <RVAEVLEG>KRAGKKGRFQGKATKMSQR>AEVQVLL*DYVSTQSTEE

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_940 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_940 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 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000266967	1 retrocopy	retro_hsap_4707,
Pongo abelii	ENSPPYG00000029909	3 retrocopies	retro_pabe_3654, retro_pabe_3655, retro_pabe_458,
Ictidomys tridecemlineatus	ENSSTOG00000000481	1 retrocopy	retro_itri_940 ,