RetrogeneDB ID: retro_cpor_271

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_112:1224845..1226083(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CTPS1
• Ensembl ID: ENSCPOG00000003389
• Aliases: None
• Description: None

Sequence

>retro_cpor_271
GACAGTGGTGACATGTTTGTTCTGGACAGCAGTGGGGAAGTTGACTTGGACTTGGGGAACTAGGAGCGGTTCCTTGACAT
CCGCCTCTCCAAGGACAACCATCTGACCACTACAAAATCTACCAGCGCGTCATTAACAAGGAATGCAAAGGGGACTACTT
GCGGAAGACTGTACAAGTTGTCATACATCACATCAAAGATGCAATCCAAGATTGAATGATGAAACAGGCTTTAGTACATG
TAGATGAAGATAGCCTGGAACCTCTAGTGTGTGTCATTGAGCTCGTGGGACAGTGGTAGATATTGAAAGCATGTCCAACA
TCAAGGCCTTTCGGCAGTTCCAGTCCAAGATTAAAAAGAACTGTTGTAATAACCATGTCAGTCTAGTTCTTCAGCCAAGT
TAAACAGGGGAACAGAAGACAAAATCCACCCAGAACAGTGTTTGGGAACTTAAGAGGTCTCGGACTCACCCCAGGCCTGG
TTGTGTACAGGTGCTCAAATGCTCTGGACACATCCATGAAAGAAAAAATATCATTGTTCAGCCATGTGGAACCTGAACAA
GTGATTCATGATGTCTCCACTATCTACTGAGTTCCCTTGTTGTTAGAATAGCAAAGGGTTGTAGATTATTTTCTTTGAAT
ACTTGAACTTCCTGTTGAGAGGGAGCCAGGAAAAATGCTGATGAAGTGGAAAAAGGTGGCAGACAGACATGATCAATCGC
TGGAGATGTGCTCTATTACTGTTGTGGGCAAATACTCCTAATTTTCGGACTCATATGCCTCAGTCATTAAAGCAATAGAG
CATTCTGCATTGGCAATCAACCACAAGTTGGAAGTTAAGTACATAGATTCCATGGACCTGGAGCTGAGCATCATGCAGGA
AGAGCCCACGTGCTACCATGAGGTGTGGCAGAAGCTCTGTAGTGCCCATGGGGTGCTGGTTCCAGGGGGGTTTAGTGTTT
GATGAACTGAAGGAAAAATCCAAGCAATTTTCTAGACTCAAAAACAGAGAAAGCTTTTTATGGATGTGTGCTTATGGATG
CATTTGGCAGTGGTTGAATTTTCAAGAAACGTGTTGGAATGGCAAGATGCCAACTCTGCAGAGTGTGATCCTAAGACCAA
TTACCCCATGCTCATAGAAAAGCCAGAGCAGAACACTGGGCATAAGGGCACAGCCATGAGGCCAGGCAAGCAGAAAACCA
TGTGCCAGATCAAGAACTCCGTCATGAGGAAACTATGG

Alignment

ORF - retro_cpor_271 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.22 %
• Parental protein coverage: 70.22 %
• Number of stop codons detected: 10
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EHGEVFVLDDGGEVDLDLGNYERFLDIRLTKDNNLTTGK-IYQHVINKERKGDYLGKTVQVV-PHITDAI
          ..G..FVLD..GEVDLDLGN.ERFLDIRL.KDN.LTT.K.IYQ.VINKE.KGDYL.KTVQVV..HI.DAI
Retrocopy DSGDMFVLDSSGEVDLDLGN*ERFLDIRLSKDNHLTTTK<IYQRVINKECKGDYLRKTVQVVIHHIKDAI

Parental  QDWVMKQALVPVDEDGLEPQVCVIEL-GGTVGDIESMPFIEAFRQFQFKVKKENFCNIHVSLVPQPSSTG
          QD..MKQALV.VDED.LEP.VCVIEL..GTV.DIESM..I.AFRQFQ.K.KK.N.CN.HVSLV.QPS.TG
Retrocopy QD*MMKQALVHVDEDSLEPLVCVIEL<RGTVVDIESMSNIKAFRQFQSKIKK-NCCNNHVSLVLQPS*TG

Parental  EQKTKPTQNSVREL-RGLGLSPDLVVCRCSNPLDTSVKEKISMFCHVEPEQVICVHDVSTIYRVPLLLEE
          EQKTK.TQNSV.EL.RGLGL.P.LVV.RCSN.LDTS.KEKIS.F.HVEPEQVI..HDVSTIY.VPLLLE.
Retrocopy EQKTKSTQNSVWEL>RGLGLTPGLVVYRCSNALDTSMKEKISLFSHVEPEQVI--HDVSTIY*VPLLLE*

Parental  QGVVDYFLRRLDLPVERQPRKMLMKWKEMADRYDRLLETCSIALVGKYTKFSDSYASVIKALEHSALAIN
          Q.VVDYFL..L.LPVER.P.KMLMKWK..ADR.D..LE.CSI..VGKY..FSDSYASVIKA.EHSALAIN
Retrocopy QRVVDYFL*ILELPVEREPGKMLMKWKKVADRHDQSLEMCSITVVGKYS*FSDSYASVIKAIEHSALAIN

Parental  HKLEIKYIDSTDLELSTMQEDPVRYHEAWQKLCSAHGVLVPGGFGVRGTEGKIQAISWARKQRKPLLGVC
          HKLE.KYIDS.DLELS.MQE.P..YHE.WQKLCSAHGVLVPGGF.V..TEGKIQAI....KQRK....VC
Retrocopy HKLEVKYIDSMDLELSIMQEEPTCYHEVWQKLCSAHGVLVPGGFSV**TEGKIQAIF*TQKQRKLFMDVC

Parental  LGMQLAVVEFSRNVLGWQDANSTEFDPKTSHPVVIEMPEHNPGQMGGTMRLGKRRTLFQTKNSIMRKLY
          L.M.LAVVEFSRNVL.WQDANS.E.DPKT..P..IE.PE.N.G..G..MR.GK..T..Q.KNS.MRKL.
Retrocopy LWMHLAVVEFSRNVLEWQDANSAECDPKTNYPMLIEKPEQNTGHKGTAMRPGKQKTMCQIKNSVMRKLW

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	13.34 RPM
SRP017611_kidney	0.00 RPM	7.75 RPM
SRP017611_liver	0.00 RPM	1.26 RPM
SRP040447_lung	0.00 RPM	13.67 RPM
SRP040447_skeletal_muscle	0.00 RPM	18.74 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_271 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_271 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005540	1 retrocopy	retro_chof_2469,
Cavia porcellus	ENSCPOG00000003389	1 retrocopy	retro_cpor_271 ,
Otolemur garnettii	ENSOGAG00000015398	1 retrocopy	retro_ogar_1936,