RetrogeneDB ID: retro_itri_1721

Retrocopy location

• Organism: Squirrel (Ictidomys tridecemlineatus)
• Coordinates: JH393665.1:215980..216767(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPAP2C
• Ensembl ID: ENSSTOG00000019777
• Aliases: None
• Description: phosphatidic acid phosphatase type 2C [Source:HGNC Symbol;Acc:9230]

Sequence

>retro_itri_1721
ACTCTATCCTGGGCTATTCTGACACTGGTGGAAGCCTCATACAAGTAACGGTTCTACTGCAAAGATGACTCCATCTGATG
CCCCTACCACCCAGACACCATGAACCATGGGCTCATGGTTATGGTCACCATCACAGCCACCATTATCCTGGTCTCCCCAG
AGATAGCCTTCCTGGTGTGCACCAATGGCCTCTACTCCCACTCCCTCTCCAATAACGATGTGGCTTTCCTCTACAAGGTG
CTGGGCACCTTCCTGTTTGAGGTGTCCATGAGCTAGTCCTTGATGGACCTGGCCAAGTACATAAATAGTTGTCTGCACCC
CAACTTCCTGGCCGTCTGCGACCCAGACTAGAGCTGGGTCAACTGTTCGGTCTATGTGCAGCTGGAGAGAATGTGCAGGG
AGAGACCTGCCAACGTCACTGAGGCCAGACTTTCCTCCTTCTGTGGACACTCCTCCGCTGGGATGTAGTGCATGCTGTTC
TTGGCTGTTCTTCCAGATGCAGCTCTGTGGGAACTTGGCGCAGCTGCTGTGGCCTACTGTGCAGTTCTCCCTGGTGGCTT
TTGCCCTGTACATGGGCTACACCCCCGTGTTGGACCACAAGCACCAGTGCCATGATGTCCTCATTAGCCTCCTACCAAGG
TCATTGGAAACTGGCCTCACTTTTTGGTAATTCTCAGACTTCTTCGAAGCCCAACACCCTCATCCCTGCCTGGAGGAGAT
GGCAGAGCACTAGCCCAACCTGTGATTGTAGTTGACTGTGGGCGAGGCTATGCACAACCACCAAGGC

Alignment

ORF - retro_itri_1721 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.91 %
• Parental protein coverage: 91.64 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SLPFAILTLVNTPYKRGFYCGDDSIRYPYRPDTITHGLMAGVTITATVILVSAGEAYLVYTDRLYSRSDF
          .L..AILTLV...YK..FYC.DDSI..PY.PDT..HGLM..VTITAT.ILVS...A.LV.T..LYS.S..
Retrocopy TLSWAILTLVEASYK*RFYCKDDSI*CPYHPDTMNHGLMVMVTITATIILVSPEIAFLVCTNGLYSHSLS

Parental  NNYVAALYKVLGTFLFGAAVSQSLTDLAKYMIGRLRPNFLAVCDPDWSRVNCSVYVQLERVCRGSPANVT
          NN.VA.LYKVLGTFLF....S.SL.DLAKY....L.PNFLAVCDPD.S.VNCSVYVQLER.CR..PANVT
Retrocopy NNDVAFLYKVLGTFLFEVSMS*SLMDLAKYINSCLHPNFLAVCDPD*SWVNCSVYVQLERMCRERPANVT

Parental  EARLSFYSGHSSFGMYCMLFLALYVQARL-CGKW-ARLLRPTVQFFLVAFALYVGYTRVSDHKHHWSDVL
          EARLS...GHSS.GM.CMLFLA....A.L..G.W.A.LL.PTVQF.LVAFALY.GYT.V.DHKH...DVL
Retrocopy EARLSSFCGHSSAGM*CMLFLAVLPDAAL<VGTW<AQLLWPTVQFSLVAFALYMGYTPVLDHKHQCHDVL

Parental  VGLLQGALVAGLTVRYVSDFFKARPLRPCLEEAVERKPSLSLTLTVGEASHNHRG
          ..LL...L..GLT....SDFF.A....PCLEE..E..P.L.L.LTVGEA.HNH.G
Retrocopy ISLLPRSLETGLTFW*FSDFFEAQHPHPCLEEMAEH*PNL*L*LTVGEAMHNHQG

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_1721 retrocopy.

TSS

Ictidomys tridecemlineatus was not studied using FANTOM5 data.

Lab

retro_itri_1721 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019734	1 retrocopy	retro_cfam_397,
Felis catus	ENSFCAG00000024319	1 retrocopy	retro_fcat_483,
Ictidomys tridecemlineatus	ENSSTOG00000019777	2 retrocopies	retro_itri_1139, retro_itri_1721 ,