RetrogeneDB ID: retro_itri_783

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393322.1:5291581..5292382(+)
• Located in intron of: None

Retrocopy information

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

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_783
GCCTCCGAAGTACAGCAGCTGCTCCATAACAAATTTGTGGTCATCCTGGGAGACTCGGTGCAGAGGGCCGTGTACAAAGA
CCTGGTGCTCCTGCTGCAGAAGGACTGCTTGCTCACTCCCAGCCAACTCAAGGCCAAGGGCGAACTGACCTTTGAACAGG
ACAAGCTGGTGAAAGGAGGTCAGCTGGGCCCCTTGCACAATGGCACCAACTACCGCGAGGTCCGCCAGTTTAGCTCAGAT
CACCATCTAGTGCGCTTTTACTTCCTCACGCGCGTTTACTCCAAGTACCTGGAGGCCATCTTGGAGGAACTCCAGTCTGG
TGAGCATGCCCCGGACCTGATCATCATGAACTCCTGCCTCTGGGATGTCTCCAGGTATGGTCCGCACTCCTGGAACAGCT
ATCTGCAGAACCTGGAGAACCTGTTTGGGCGATTGGGCGAAGTTCTGCCTGAGTCTTGCCTCCTGGTGTGGAACACGGCC
ATGCCTGTGGGTAAGAAAATTACCGCACGCTTTCTGCCACGCAAGCCCCTGCCCTGGGCCATCCCTCTGCGAAGGATCGT
GGTGCATGCCAACTTCTACAGCTCCATCAAGGCAAGTAATCATGGCTTCGATGTGCTAGACTTGCATTTCCACTTTCGTC
ATGCTTGGAATTGCCTGCAGTCAGATGGGGTGCACTGGAATGAGCACGCACACCGCCAGCTCTCCTACCTGCTGCTGACC
CACGTGGCTGAGGCCTGGGGTGTGGAGCTACCCTGCCGCCCACCCGCACCCATAGGCGAGCTGATCCAGGACGCTCCTGA
G

Alignment

ORF - retro_itri_783 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.63 %
• Parental protein coverage: 59.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ASEVQQLLHNKFVVILGDSIQRAVYKDLVLLLQKDSLLTAAQLKAKGELSFEQDQLVAGGQLGELHNGTQ
          ASEVQQLLHNKFVVILGDS.QRAVYKDLVLLLQKD.LLT..QLKAKGEL.FEQD.LV.GGQLG.LHNGT.
Retrocopy ASEVQQLLHNKFVVILGDSVQRAVYKDLVLLLQKDCLLTPSQLKAKGELTFEQDKLVKGGQLGPLHNGTN

Parental  YREVRQFCSGSGHHLVRFYFLTRVYSEYLEDVLEELTYGP-APDLVIINSCLWDLSRYGRCSMESYRENL
          YREVRQF...S.HHLVRFYFLTRVYS.YLE..LEEL..G..APDL.I.NSCLWD.SRYG..S..SY..NL
Retrocopy YREVRQF--SSDHHLVRFYFLTRVYSKYLEAILEELQSGEHAPDLIIMNSCLWDVSRYGPHSWNSYLQNL

Parental  ERVFVRMDQVLPDSCLLVWNMAMPLGKRITGGFLLPELQPLAGTLRRDVVEGNFYSATLAGDHCFDVLDL
          E..F.R...VLP.SCLLVWN.AMP.GK.IT..FL.....P.A..LRR.VV..NFYS...A..H.FDVLDL
Retrocopy ENLFGRLGEVLPESCLLVWNTAMPVGKKITARFLPRKPLPWAIPLRRIVVHANFYSSIKASNHGFDVLDL

Parental  HFHFRHAVRHRHRDGVHWDQHAHRHLSHLLLTHVADAWGVELPKRDHPP-DPWIEDWPE
          HFHFRHA......DGVHW..HAHR.LS.LLLTHVA.AWGVELP.R...P....I.D.PE
Retrocopy HFHFRHAWNCLQSDGVHWNEHAHRQLSYLLLTHVAEAWGVELPCRPPAPIGELIQDAPE

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_783 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_783 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,