RetrogeneDB ID: retro_cpor_369

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_133:2568717..2569441(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSCPOG00000000222
• Aliases: None
• Description: None

Sequence

>retro_cpor_369
GATGGCTGCTGGTCCCTCTCACAGCAGGTGGCCGGGCACTAGTGCAGGAAGGACAAAGTAGATACATTGCAGCATCCATA
TGGCACAGTCTTGGTACAGTTACAGCCACCCCCAAGGGATCCAAGAAAGCCAGACTCTTATATGGTTTATGTTGCTTATT
GTAGTAATAGTGTTCTTCTAGTGCTACAAAATATTTGTCAAAATATTGTACCTGGTCACCTCCCTCTGCATCAAATGATT
TATGCCTAAAGCTGGAATATATGACCCATAAATGGAATAAGCCTTGTATAATGGATGTAAATGTAAAGACAGGATGAGAA
AGCTATGATCGTCTTGCCTCATCCAAGAGGATTCAGCAATAGGTCAGCAAGTGCCCATTAATGGAAGAGATTGGATCCTT
GGTACTTGGCACGAAGGTTTATCATGTTCATTCTGATAGCCATGAGATGCTAAACTAGCACTATGGAAGATGCCTAACAA
GACAGACTATAATGAAAGGGCTCTTTAAGTGTTTTCATAATGGGTTCAGCTTAAGAAAAGATGCTGTTGCTACCAGTATT
CAGAAGACAGAAAATTTCTGCAGTGGTTTGAAACCAGAAACAGCTTTTATGCAATTTCATTACTATTTGTTTATGACAGG
TCACCTCAGCCAACCACTACAAAATCAAATGACAGAACTTTGGCAGAAAAGTTTTTGCCCAAAGGACAACTATTACACAC
AGAA

Alignment

ORF - retro_cpor_369 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.53 %
• Parental protein coverage: 62.47 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NGCVPLSHQ-AGHMYGKDKVGILQHPDGTVLKQLQPPPRGPRELEFYNMVYAADCSDGILLELR-KYLPK
          .GC..LS.Q.AGH...KDKV..LQHP.GTVL.QLQPPPR.PR....Y.MVY.A.CS...LL.L..KYL.K
Retrocopy DGCWSLSQQVAGH*CRKDKVDTLQHPYGTVLVQLQPPPRDPRKPDSY-MVYVAYCSNSVLLVLQ<KYLSK

Parental  YYGVWSPPTAPNDLYLKLEDVTHKFNRPCIMDV--KIGRKSYDPFASSEKIQQQVSKYPLMEEIGFLVLG
          Y...WSPP.A.NDL.LKLE..THK.N.PCIMDV..K.G..SYD..ASS..IQQ.VSK.PLMEEIG.LVLG
Retrocopy YC-TWSPPSASNDLCLKLEYMTHKWNKPCIMDVNVKTG*ESYDRLASSKRIQQ*VSKCPLMEEIGSLVLG

Parental  MRVYHVHSDSYETQNQHFGRSLTKETIKDGISKFFHNGFSLRKDAIAASIEKIE-KILQWFESQKQLNFY
          ..VYHVHSDS.E..N.H.GR.LT..TI..G..K.FHNGFSLRKDA.A.SI.K.E.K.LQWFE......FY
Retrocopy TKVYHVHSDSHEMLN*HYGRCLTRQTIMKGLFKCFHNGFSLRKDAVATSIQKTE<KFLQWFETRN--SFY

Parental  ASSLLFVYEGSSQPTTTKSNDRTLAEKFLSKGQLSDTE
          A.SLLFVY..S.QPTTTKSNDRTLAEKFL.KGQL..TE
Retrocopy AISLLFVYDRSPQPTTTKSNDRTLAEKFLPKGQLLHTE

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	4.31 RPM
SRP017611_kidney	0.00 RPM	6.07 RPM
SRP017611_liver	0.00 RPM	4.31 RPM
SRP040447_lung	0.00 RPM	6.33 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_369 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_369 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000011011	1 retrocopy	retro_apla_14,
Cavia porcellus	ENSCPOG00000000222	1 retrocopy	retro_cpor_369 ,
Erinaceus europaeus	ENSEEUG00000009958	1 retrocopy	retro_eeur_110,
Homo sapiens	ENSG00000151151	2 retrocopies	retro_hsap_1244, retro_hsap_2032,
Gorilla gorilla	ENSGGOG00000008790	1 retrocopy	retro_ggor_1464,
Myotis lucifugus	ENSMLUG00000015030	1 retrocopy	retro_mluc_518,
Nomascus leucogenys	ENSNLEG00000012319	2 retrocopies	retro_nleu_2419, retro_nleu_2622,
Pongo abelii	ENSPPYG00000002433	3 retrocopies	retro_pabe_1035, retro_pabe_1086, retro_pabe_1689,
Pan troglodytes	ENSPTRG00000002516	2 retrocopies	retro_ptro_1351, retro_ptro_855,