RetrogeneDB ID: retro_itri_1190

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393396.1:3829903..3830623(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSTOG00000025463
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PCED1A
• Ensembl ID: ENSSTOG00000016356
• Aliases: None
• Description: PC-esterase domain containing 1A [Source:HGNC Symbol;Acc:16212]

Sequence

>retro_itri_1190
GCCACCATGGCCCACCTGCGAGCCTGCAAAGTCAGGCAGCTGCTTCACAAGTTCGCAGTTGTCATGGGGGACTCCATCCA
ACGGGCGGAGTACAAGGACCTGGTCCTCCTACTGCAGAAGGACTGCCTGCTCTCTTCCAGTCAGCTGAAGACCAGGGGCG
AAATAAGCTTCGAGCACGACGTGCTGCTGGAGGGTGGCAGGTGGGGCCGCATGCACAACAGCCCCCACTACCGCGAGGTT
CGCCAATTCTGCTCCAGCCACCACCTGGTGCGCTTCTACTTCCTTACGCGTGCGTACTCGCCTTACTTCGAGGATATCCT
GGCAGAGCTGCGGTGGGGCGAGCACGCCCCCGACGTGGTCATCCTGAACTCTTGCCTCTGGGACCTCTCCAGATACGGCC
ATGATTTCCAAAGGAGCTACCGGGAAGACGTGGAGAGCCTGTTCCGGCGCCTGGACCAGGTCCTGCCCCAGTCCTGCCTA
CTGGTGTGGAACACAGCCATGCCTGTGGCAGAAGTCGTCTCTGGAGTCTTCCTTGCCTCGGAAGGCGAGACCTGCCGGAC
CAGCCTGCGGGAAGACGTGACGGAGGCCAACTTCTACAGCTGTATGGAGGCGGTCAGGCATGGCTTCGATGTGCTGGACC
TCCATTTCCACTTGTGCCACGCGGGGCAACACCGGCAGTCAGATGGCGTGCACTGGGACAAGCGCGCACGGGCACCTCTC

Alignment

ORF - retro_itri_1190 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.32 %
• Parental protein coverage: 53.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SAMVHFQASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLG
          ..M.H..A..V.QLLH.KF.V..GDSIQRA.YKDLVLLLQKD.LL...QLK..GE.SFE.D.L..GG..G
Retrocopy ATMAHLRACKVRQLLH-KFAVVMGDSIQRAEYKDLVLLLQKDCLLSSSQLKTRGEISFEHDVLLEGGRWG

Parental  ELHNGTQYREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYGP-APDLVIINSCLWDLSRYGRCSM
          ..HN...YREVRQFCS...HHLVRFYFLTR.YS.Y.ED.L.EL..G..APD.VI.NSCLWDLSRYG....
Retrocopy RMHNSPHYREVRQFCSS--HHLVRFYFLTRAYSPYFEDILAELRWGEHAPDVVILNSCLWDLSRYGHDFQ

Parental  ESYRENLERVFVRMDQVLPDSCLLVWNMAMPLGKRITGGFLLPELQPLAGTLRRDVVEGNFYSATLAGDH
          .SYRE..E..F.R.DQVLP.SCLLVWN.AMP......G.FL..E.......LR.DV.E.NFYS...A..H
Retrocopy RSYREDVESLFRRLDQVLPQSCLLVWNTAMPVAEVVSGVFLASEGETCRTSLREDVTEANFYSCMEAVRH

Parental  CFDVLDLHFHFRHAVRHRHRDGVHWDQHAHRHL
          .FDVLDLHFH..HA..HR..DGVHWD..A...L
Retrocopy GFDVLDLHFHLCHAGQHRQSDGVHWDKRARAPL

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_1190 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1190 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003863	1 retrocopy	retro_btau_182,
Cavia porcellus	ENSCPOG00000025475	2 retrocopies	retro_cpor_343, retro_cpor_79,
Equus caballus	ENSECAG00000016497	1 retrocopy	retro_ecab_87,
Felis catus	ENSFCAG00000002886	1 retrocopy	retro_fcat_18,
Homo sapiens	ENSG00000132635	2 retrocopies	retro_hsap_2207, retro_hsap_82,
Microcebus murinus	ENSMICG00000016578	2 retrocopies	retro_mmur_163, retro_mmur_278,
Myotis lucifugus	ENSMLUG00000028662	2 retrocopies	retro_mluc_222, retro_mluc_647,
Macaca mulatta	ENSMMUG00000005200	2 retrocopies	retro_mmul_333, retro_mmul_341,
Mus musculus	ENSMUSG00000037773	2 retrocopies	retro_mmus_1001, retro_mmus_332,
Otolemur garnettii	ENSOGAG00000004701	1 retrocopy	retro_ogar_81,
Pongo abelii	ENSPPYG00000010833	2 retrocopies	retro_pabe_192, retro_pabe_2080,
Pan troglodytes	ENSPTRG00000013185	1 retrocopy	retro_ptro_105,
Pteropus vampyrus	ENSPVAG00000006834	1 retrocopy	retro_pvam_9,
Sus scrofa	ENSSSCG00000007168	1 retrocopy	retro_sscr_23,
Ictidomys tridecemlineatus	ENSSTOG00000016356	2 retrocopies	retro_itri_1190 , retro_itri_783,
Tursiops truncatus	ENSTTRG00000003464	1 retrocopy	retro_ttru_16,