RetrogeneDB ID: retro_cpor_657

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_21:18520422..18521809(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UTP18
• Ensembl ID: ENSCPOG00000001477
• Aliases: None
• Description: None

Sequence

>retro_cpor_657
AGGCTGGGCATCTCTGGGGGCAAACCAGCCATGGAGCTGTGTGGAGAAGAGCTGGTCTTTGACACCATGGGGTGGGTGGG
GGACCAGGAGGACGCACTTCTGTGGTACTGCAGGGCGCGCAGGTTCAGGTACAAGAAGACTCCATGACTCAGAAGTGGAA
ATGAAGCAAAAGATAATTTTTCCCCTTGGAAGGAACCAGTTTGGGTGGATGAAGAAGATGAAGATGAGGAAATGGTTGAC
TCGAGAAACAACCGTTTTAGGAAAGCTATGGTGAAAAAGTACCAGGGAAAGTAAACTTTCCAAAGAGAAGCTTCAAGGAG
ACAAAGAAGAATTCTAGCATGCCCTGCGGTGAGTGCCTGCCTAGGCAGAACTTAATTAGCAGAAAATATCTTCAGATGAT
GAAAGTGAAGAGGATGAAGCTAATTTGCTGCAAAGGACTGGGAATTTTTTTCCATATGAGTTTCTCTTGCAAGAGGAATC
TTGACAATAAAGAACTGCTAGCTTGTGGATACAGAGAGCCCTACCACTGCCCAGATCTCATCAGTCCAGTTCCTTCCCTG
TGCCCAGGTTGTGGCAGCTGCTGGCTTAGATAACACCTCTTCACTGTTTCAGGTTGATAGCAAAACAAATCCCTAAATCT
AGAGCATCTATTTGGAGGTTTCCAATCTTTATAGCTTGTTTTAGTGCTAATGGAGTGCAGGTTTTAGCAGGAAACACTCA
CAGCAGGATTCTTTATGTCTATGATATTCAGGCTGGGAAGTTAAGTCCTATGCATCAAGTGAGAGTCTTGAAAGAAAGAA
TATTGAGAACATTTGAAGTCTCCCCAGATGGACCCTTCATGCTCATTCATGGTATTGCTGGCGACTCTTATTTGCTGGCA
ATGAAGACCAAAGAGCTGATTGGAAGTATGAAGGTTACTGAAGGGGTTTCAGCATCTGTGTTTACTTCAGATAGTAAGAA
AATACACACCTATGCTGGGGACCAGAAAGTTTATGTTTGAGATGTGAACTCTAGGAATCGCCTTAACAGATTTGCCGATG
AAGGCAGTTTATGTGGATTAAGCATTGCCATATCGAGGAGTGGGCAGTAGGTCGCTTGTGGTTCTGGTTTTGGAATAGTA
AACATTTACAGTCAAGATTCTTGTGTTCAAGAAACAAACCCAAAGCCAATAAAAGCCATAATGAGCTTGGTAACTGGTGT
TACATCTCTGGCCTTCAATCCTGCTTCAGAAATTTTGGCAGTTGCTTCAGAAAAGATGATGGGAGTGGTCCGATTGGTTC
ATCTTCAATCCTGTACAGTATTTTCTAACTTTCTAGTTGTTAAAAAGGAGAATATTTCTCATGCCCATTTTGTGGATTAT
TCTCCCAGAGGTGGCTGCTTTGCTTTA

Alignment

ORF - retro_cpor_657 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.49 %
• Parental protein coverage: 95.26 %
• Number of stop codons detected: 8
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RLTLEEDKPAVERCLEELVF---GDVGGDEDALLRS-LRGARVQVHEDS-DDAEVE-NEAKGNFPPQKRP
          RL.....KPA.E.C.EELVF...G.VG..EDALL...L.GA.VQV.EDS..D.EVE.NEAK.NF.P.K.P
Retrocopy RLGISGGKPAMELCGEELVFDTMGWVGDQEDALLWY<LQGAQVQVQEDS<HDSEVE<NEAKDNFSPWKEP

Parental  VWVDEEDEDEEMVDMRNNRFRKDMMK-NASESKLSKEKLQKRLKEEFQHAMGGVPAWAETSKRKTSSDDE
          VWVDEEDEDEEMVD.RNNRFRK.M.K....ESKLSKEKLQ...KEEF.HA...VPA.AE....K.SSDDE
Retrocopy VWVDEEDEDEEMVDSRNNRFRKAMVK>STRESKLSKEKLQGD-KEEF*HALR*VPA*AELN*QKISSDDE

Parental  SEEDEDDLLQRTGNFL-STSVSLPRGILKMKNCQHANAERPTTAQISSVQFHPCAQVVMVAGLDNAFSLF
          SEEDE..LLQRTGNF..S..VSL.RGIL..KNC.....E.PTTAQISSVQF.PCAQVV..AGLDN..SLF
Retrocopy SEEDEANLLQRTGNFF<SI*VSLARGILTIKNC*LVDTESPTTAQISSVQFLPCAQVVAAAGLDNTSSLF

Parental  QVDGKTN-PKIQSIYLEKFPIFKACFSANGEQVLATSTHSRVLYVYDMLAGKLIPVHQVRGLKERMVKSF
          QVD.KTN.PK........FPIF.ACFSANG.QVLA..THSR.LYVYD..AGKL.P.HQVR.LKER....F
Retrocopy QVDSKTN>PKSRAS-IWRFPIFIACFSANGVQVLAGNTHSRILYVYDIQAGKLSPMHQVRVLKERILRTF

Parental  EVSPDGSFLLINGIAGYSHLLSMKTKELIGSMKINGRVSASAFTSDSKKIYTYSGEGEVYIWDVNSRKCL
          EVSPDG.F.LI.GIAG.S.LL.MKTKELIGSMK....VSAS.FTSDSKKI.TY.G...VY..DVNSR..L
Retrocopy EVSPDGPFMLIHGIAGDSYLLAMKTKELIGSMKVTEGVSASVFTSDSKKIHTYAGDQKVYV*DVNSRNRL

Parental  NRFVDEGSLCGLSIATSRNGQYVACGSGCGVVNIYSQDSCLQETNPKPIKAIMNLVTGVTSLAFNPATEI
          NRF.DEGSLCGLSIA.SR.GQ.VACGSG.G.VNIYSQDSC.QETNPKPIKAIM.LVTGVTSLAFNPA.EI
Retrocopy NRFADEGSLCGLSIAISRSGQ*VACGSGFGIVNIYSQDSCVQETNPKPIKAIMSLVTGVTSLAFNPASEI

Parental  LAIASKKMKEAVKLVHLPSCTVFSNFPIVKRKTISLVHSMDFSPRGGYFAL
          LA.AS.KM...V.LVHL.SCTVFSNF..VK...IS..H..D.SPRGG.FAL
Retrocopy LAVASEKMMGVVRLVHLQSCTVFSNFLVVKKENISHAHFVDYSPRGGCFAL

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	46.99 RPM
SRP017611_kidney	0.00 RPM	41.25 RPM
SRP017611_liver	0.00 RPM	19.72 RPM
SRP040447_lung	0.00 RPM	42.75 RPM
SRP040447_skeletal_muscle	0.00 RPM	19.44 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_657 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_657 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 6 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000001477	1 retrocopy	retro_cpor_657 ,
Homo sapiens	ENSG00000011260	1 retrocopy	retro_hsap_1882,
Gorilla gorilla	ENSGGOG00000017061	1 retrocopy	retro_ggor_1379,
Myotis lucifugus	ENSMLUG00000016938	1 retrocopy	retro_mluc_2308,
Mustela putorius furo	ENSMPUG00000015582	1 retrocopy	retro_mputfur_646,
Vicugna pacos	ENSVPAG00000010164	1 retrocopy	retro_vpac_170,