RetrogeneDB ID: retro_itri_185

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: AGTP01150962.1:257..1313(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PTGIS
• Ensembl ID: ENSSTOG00000019624
• Aliases: None
• Description: prostaglandin I2 (prostacyclin) synthase [Source:HGNC Symbol;Acc:9603]

Sequence

>retro_itri_185
CTGGGCGACGCCACGGAAGGGGCCAGCAGCTGGCGGGAGGTGGACCTCCTGGACCTCTGCTATGGCTCTCTGCTCAGAGC
CGGCTACCTGACCCTGTATGGAGTGGAGGCGTCCCCACGCACCTAGGAGAGCCAGGCCCAGGACAGAGCCCACTCGGCCA
ACGTCTACCACACCTTCCGCCAGCTGGACCTGATGCTCCCCAAGCTGGCGCGAGGCTCCCTGTCAGTGGGGGATAATGAC
CGTGTGTGCAGCGTCAAAGCCCACCTGTGGAAGCTGCTGTCCCCCGTCAGGCTGGCCACGCGAGCCCAGCGGAGCAGCTG
GCTGGAGAGCTACCTGCGGCACCTGGAGGAGCTGGGGGTTTCGGAGGAGATGCAGGCGCGGGCCCTGGTGCTGCAGCTGT
GGGCTACACAGGGAAACATGGGGCCTGCTGCCTTCTGGCTCCTTCTCTTCCTCCTCAAGAATCCCGAGGCCCTGGCTGCT
GTCCACGGGGAACTCGAGGGCGTCCTCTGGAGAGCAGAGCAGCCCGGCTCACAGATGACCACCCTCCCGCAGAAGGTCCT
AGACAACATGCCCGTGCTCGACAGCGTGCTGGATGAGACCCTCATGCTCACAGCTGCACCCTTCATCACCCGGGAGGTGG
TGGTGGACATGGCTATGCCCATGGCCGATGGGCGGGAATTCTCTCTGCGACATGGTGACCGCCTCCTCCTCTTCCCCTTC
CTGAGTCCCCAGAGAGACCCTGACATCTACTCGGATCCTGAGACGTTTAAATACGACCTGTTCCTGAACGCCGACGGGTC
GGAGAAGAGAGACTTCTACAAGGACGGGAAGCGGCTGAAGCACCCTAGCATGCCCTGGGGGGCGGGCCACAACCAGTGCC
TGGGCAGGGGCTACGCCGTCAGCAGCATCAAGCAGTTCCTGGTCCTGGTGCTGACGCACTGCGACCTGGAGCTGATCCGG
GCAGACGTGGAGGTCCTCGAGTTTGACCTCAGCAGGTACGGCTTCGGCCTGATGCAGCCAGAACTTGACGTGCCTGTGCG
ATTCCGCGTCCGGCCC

Alignment

ORF - retro_itri_185 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.41 %
• Parental protein coverage: 71.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVDATEGASGWREVGLLDLCYGSLLRAGYLTLYGVEASPRTPESQAQDRAHSADVYHTFRQLDLMLPKLA
          L.DATEGAS.WREV.LLDLCYGSLLRAGYLTLYGVEASPRT.ESQAQDRAHSA.VYHTFRQLDLMLPKLA
Retrocopy LGDATEGASSWREVDLLDLCYGSLLRAGYLTLYGVEASPRT*ESQAQDRAHSANVYHTFRQLDLMLPKLA

Parental  RGSLSVGEHPGVPGVKARGQAWACVAKARACAGSPLQPRWSLSYSVHIRSLVVEAKMFTEVFSLGTWVCG
          RGSLSVG....V..VKA....W......R..........W..SY..H...L.V...M......L..W...
Retrocopy RGSLSVGDNDRVCSVKAH--LWKLLSPVRLATRAQ-RSSWLESYLRHLEELGVSEEMQARALVLQLWATQ

Parental  GNMGPAAFWLLLFLLKNPEALAAVRGELERVLWGAEQPGSQMTTLPQKVLDNMPVLDSVLDETLRLTAAP
          GNMGPAAFWLLLFLLKNPEALAAV.GELE.VLW.AEQPGSQMTTLPQKVLDNMPVLDSVLDETL.LTAAP
Retrocopy GNMGPAAFWLLLFLLKNPEALAAVHGELEGVLWRAEQPGSQMTTLPQKVLDNMPVLDSVLDETLMLTAAP

Parental  FITREVVVDMAMPMADGREFSLRRGDRLLLFPFLSPQRDPDIYSDPETFKYDRFLNADGSEKRDFYKDGK
          FITREVVVDMAMPMADGREFSLR.GDRLLLFPFLSPQRDPDIYSDPETFKYD.FLNADGSEKRDFYKDGK
Retrocopy FITREVVVDMAMPMADGREFSLRHGDRLLLFPFLSPQRDPDIYSDPETFKYDLFLNADGSEKRDFYKDGK

Parental  RLKHPSVPWGMGHNQCLGRGYAVCSIKQFVVLVLTHCDLELVRADVEVPEFDLSRYGFGLLQPELDVPVR
          RLKHPS.PWG.GHNQCLGRGYAV.SIKQF.VLVLTHCDLEL.RADVEV.EFDLSRYGFGL.QPELDVPVR
Retrocopy RLKHPSMPWGAGHNQCLGRGYAVSSIKQFLVLVLTHCDLELIRADVEVLEFDLSRYGFGLMQPELDVPVR

Parental  FRVRP
          FRVRP
Retrocopy FRVRP

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_185 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_185 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.

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000019624	1 retrocopy	retro_itri_185 ,
Tursiops truncatus	ENSTTRG00000004297	1 retrocopy	retro_ttru_775,