RetrogeneDB ID: retro_itri_187

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: AGTP01152506.1:1..790(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCMTD2
• Ensembl ID: ENSSTOG00000010236
• Aliases: None
• Description: protein-L-isoaspartate (D-aspartate) O-methyltransferase domain containing 2 [Source:HGNC Symbol;Acc:15882]

Sequence

>retro_itri_187
ATGGGCAGTGTGGTGAGTGCTGGAGAGGACAATGATGAGCTGATTGATAATCTGAAGGGAGCCCAGTATATCCGGACGGA
ACTGGTAGAGCAGGCTTTCAGAGCTATGGATCGTGGAGATTATTATCTTGAAGAGTTTAAAGAAAATGCCTACAAGGACT
TGGCATGGAAGCATGGAAACATTCACCACTCCGCCCCATGTATCTACTCAGAGGTGATGGAGGCTCTGGATCTGCAGCCT
GGGCTCTCATTTCTGAACCTGGGCAGTTGCACTGGCTACCTCAGCTCCATGGTGGGCCTTATTCTAGGTCCTTTTGGTGT
GAACTATGTGGTGGAGCTACATTCAGATCTTATAGAGTATGCAAAGCAGAAACTGGACTTCTTCATCAGAACATGTGATA
GCTTCGACAAGTTTGACTTCTGCGAGCCCTCTTTTGTTAGTGGCAATTGCCTGGCGATTTCCCCAGATTGTTCTCAGTAT
GATCGGGTGTACTGTGGAGCAGGTGTGCAGAAAGAACATGAAGAGTACATGAAGAGTCTTCTCAAGGTTGAAGGAATTCT
GGTCATGCCCCTGGAGGAGAAGTTGACCAAGATAACGTGCATAGGCCCTTTTGCTTGGGAAACCAAAAAGATTCTGCCTG
TTTCCTTCGCTCCTCTGGTCCAGCCCTGCCACTCAGAGTCAGGAAAGTCCAGACTTGTTCAGCTACCACCATTGGCTGTC
CGCAGCCTCCAGGACTTGGCCCGCATTGCCATCAGGGGCACCATCAAGAAGGTCATTCATCAGAAAGCA

Alignment

ORF - retro_itri_187 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 73.06 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGGAVSAGEDNDELIDNLKEAQYIRTELVEQAFRAIDRADYYLEEFKENAYKDLAWKHGNIHLSAPCIYS
          MG..VSAGEDNDELIDNLK.AQYIRTELVEQAFRA.DR.DYYLEEFKENAYKDLAWKHGNIH.SAPCIYS
Retrocopy MGSVVSAGEDNDELIDNLKGAQYIRTELVEQAFRAMDRGDYYLEEFKENAYKDLAWKHGNIHHSAPCIYS

Parental  EVMEALDLQPGLSFLNLGSGTGYLSSMVGLILGPFGVNHGVELHSDVIEYAKQKLDFFIRTSDSFDKFDF
          EVMEALDLQPGLSFLNLGS.TGYLSSMVGLILGPFGVN..VELHSD.IEYAKQKLDFFIRT.DSFDKFDF
Retrocopy EVMEALDLQPGLSFLNLGSCTGYLSSMVGLILGPFGVNYVVELHSDLIEYAKQKLDFFIRTCDSFDKFDF

Parental  CEPSFVTGNCLEISPDCSQYDRVYCGAGVQKEHEEYMKSLLKVGGILVMPLEEKLTKITRIGPSAWETKK
          CEPSFV.GNCL.ISPDCSQYDRVYCGAGVQKEHEEYMKSLLKV.GILVMPLEEKLTKIT.IGP.AWETKK
Retrocopy CEPSFVSGNCLAISPDCSQYDRVYCGAGVQKEHEEYMKSLLKVEGILVMPLEEKLTKITCIGPFAWETKK

Parental  ILAVSFAPLVQPCHSESGKSRLVQLPPLAVRSLQDLARIAIRGTIKKVIHQEA
          IL.VSFAPLVQPCHSESGKSRLVQLPPLAVRSLQDLARIAIRGTIKKVIHQ.A
Retrocopy ILPVSFAPLVQPCHSESGKSRLVQLPPLAVRSLQDLARIAIRGTIKKVIHQKA

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_187 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_187 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Ictidomys tridecemlineatus	ENSSTOG00000010236	1 retrocopy	retro_itri_187 ,
Tursiops truncatus	ENSTTRG00000016870	1 retrocopy	retro_ttru_33,