RetrogeneDB ID: retro_cpor_1351

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_71:7210973..7211988(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAP9
• Ensembl ID: ENSCPOG00000027185
• Aliases: None
• Description: None

Sequence

>retro_cpor_1351
CAAGTTTTCCACACAACCTTGGCATATATGAAGAGTCAAAAAGTTAGCAAAAGAACTCCAGGATGAGCAGATAAGTGCAA
TCATAGCCCACTAAGCCAGGCGGAGATCAGAGTATTCAGGTAGCTTTGAAAGAGATACTGTTTCCTTAGGTGATTTTTCT
GATATCTCAGTAGATGAAAATTCAGTTAAAAAAATAAATTATTTTCATGTATCTGATGAAGAAAAGAGTTCTGCACAACT
GTCTTTTTTGAAAACCAATCAATCAAACAGGGAAAGAAGGAGAGGCAAGCCATAAGTGGCCATCAAGAGTCATAAAGGAC
AAGCATCTGATGTCTGTGAAGATACATGCAAATCCCTCTCTGAATCTCAAATAAAGATCAAGAATTTGAAAATGGAGAAT
TAAAATAAAACTGAAACCCAGAATTCTTCAAATCAAAAGCACCTTTTCAGAAAATAGAAGCAGTCTTGAAGCAGGTGAAT
GTTTTAGGCTTTCACCTCAGCCCCGGAGCTTGTTAAAAAGAGTAGCCATGTGGAGGAGAAGGAAGAACAAAGGGAAGAGA
AGGAAACTGTCTTGGTGAGGACATGGATTCTGCGTCTTCCTCCCTTCCCCACGCTGAGTGTCAGACAGCTTGAAGCGGAG
AAAGATGTGTTCTCTGCAGACCTTGGTCTTGAGAAACAGAATCCGTTATTTATACGCCTTCATCATCATCTCTTAAAGAA
AGCCTTGGAAGACTCTTTCCACCCGGATCTGACGAGAAGGCACCAGAACAGATCAGAATGGAGAAGTTGCGGAAACCATG
ATTCCTGGAAATTGGATAAAAATGAAGAAAATGAAGTTCTGGTAGACTTGGTTTCTCTTGAACTTGAGAAACTCAAGGAA
AAATGAGGTGACCACTGATGACCTTGAAGATGACAAGGAGAAGGCTGGGCTAGAGGTGAATGAGGAATTCAGAGCTGCTC
CCTGCCACTTAAATCTCTGAAGACTCTTGGACCTACCAATGCAAAGGCACCTGCA

Alignment

ORF - retro_cpor_1351 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.5 %
• Parental protein coverage: 55.29 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 11

Retrocopy - Parental Gene Alignment:

Parental  EIFSTTLAYTKSP-KVTKRTTFQDELIRAIIARSARQRSSEYSDDFESDVVSLGDLSDTSVDENSVKKKI
          ..F.TTLAY.KS..K..K....QDE.I.AIIA..AR.RS.EYS..FE.D.VSLGD.SD.SVDENSVKK.I
Retrocopy QVFHTTLAYMKSQ>KLAKE--LQDEQISAIIAH*ARRRS-EYSGSFERDTVSLGDFSDISVDENSVKK-I

Parental  NDFHISDDEEKNSPRPSFLKAKKSNGDIR-DEPEVAVKNCEERAPDVCENTVAGSFSE-IQNNDLEVE-K
          N.FH.SD.EEK.S...SFLK...SN...R...P.VA.K.....A.DVCE.T...S.SE.I.N.D.E.E.K
Retrocopy NYFHVSD-EEKSSAQLSFLKTNQSNRERRRGKP*VAIKSHKGQASDVCEDTCK-SLSE<ISNKDQEFE<K

Parental  ERIKIKPKPRVLSVKSTSSETSSSLEADRHFRPSPRPRSLLR-KSSHVEEKEESGEEKET-ALREDVDHA
          .RIKIK.KPR.L..KST.SE..SSLEA...FR.SP.PRSLL..KSSHVEEKEE..EEKET..L.ED.D.A
Retrocopy WRIKIKLKPRILQIKSTFSENRSSLEAGECFRLSPQPRSLLK<KSSHVEEKEEQREEKET<CLGEDMDSA

Parental  PSSLPE-LGVRQLEAEKDTSSADLGLEQQDPLF-RSPSSSPLEESLGSCLPPGPEE-ETLRIDQNGEVTE
          .SSLP..L.VRQLEAEKD..SADLGLE.Q.PLF...PSSS.L.ESLG...PPG..E.E..R.DQNGEV.E
Retrocopy SSSLPH>LSVRQLEAEKDVFSADLGLEKQNPLF<YTPSSSSLKESLGRLFPPGSDE<EGTRTDQNGEVAE

Parental  -NCNSCKLNENEEKAVLIDCVAPEIEKPNER-EVAIDDLEEGKEKDGPGLEEDFPAAP-RPLKSPRTVGP
          .N..S.KL..NEE..VL.D.V..E.EK..E..EV..DDLE..KEK.G....E.F.AAP..PLKS..T.GP
Retrocopy <NHDSWKLDKNEENEVLVDLVSLELEKLKEK>EVTTDDLEDDKEKAGLEVNEEFRAAP<LPLKSLKTLGP

Parental  TSTTAPA
          T...APA
Retrocopy TNAKAPA

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	28.64 RPM
SRP017611_kidney	0.00 RPM	10.36 RPM
SRP017611_liver	0.00 RPM	3.57 RPM
SRP040447_lung	0.00 RPM	2.52 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.18 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1351 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1351 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027185	1 retrocopy	retro_cpor_1351 ,