RetrogeneDB ID: retro_cpor_283

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_116:3586772..3587759(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM22
• Ensembl ID: ENSCPOG00000001946
• Aliases: None
• Description: None

Sequence

>retro_cpor_283
TCTCTGGGTTCCAATGCCTAAAACAGGCAGAACTGTGAAGATGCAGACTTCTTGATTCTATGCCAGATATGCCTTTGTGA
AAACCCCTATCTCCAAATGATCAAGGAAAATTACCAGAAGGAATGCAAGATCTGTGCCAGGCCATTCACAGTGTTTCACT
GTTGTTCTGAGGTCTGCATGTGCTTCAAGAAGATCTAAGTGTGCCTAACCTGCAGTAAACTCAAGAATTTCTGTCAATTA
TGCCTCTTAGACCTAGAATATGGCTTTCCCATTCAGGTTTCAGATTCAGGACTGTCTTTTAAAGATGACATTCCCATGTT
ATATGTCAACAAAGAGTACTACACACAGAATATGGAAGGGAAATTTCTAACTCTGATGGAATAAGTCCAGTTGGCACGCT
GGGAAAAGCCACATTTACTAGTGACATGCTGCTTAAGCTGGCCCAGACTGTATCCTACTCCAAAAGGAATCACCCCACAT
TTGCTCATTCTGGCTGAAAGGAGAGTGTAAGAGAGAAGAGGAGTGTCCATAAATACATGAAAAACTTACAGACCAAGACA
GCTCCCTTGCTGATCAGAACATTAAATACTGGTATTGTGGAATGAGGGACCCTGAGGCAGATAAGCTTCTAAAAGCAGGC
TTCAGCAAAGCTCTGTTTAAACCCACCCAAGGATAAGACATTTACCACATTGTATGTTATAGGTCTGGGTAGTGCCATCA
CTGAGACATACCTCAGAAATCACTTCTACCACTTGGGAGTGATCTGAACAATCACTGTTGTACAGAGGCAGCAGTGTACT
TTCATCTAGTTGGCCACAAGGCAGGCTGCAGAAATGGCTGCTGAGGAGACCTTTAATTAGCCAATTGTCAATGGCCACAG
ACTCAGCATGAAGTGGGCAAGATCCCAGGCAGCCAAGGGGAGAGAAAGAGAGAAGGATGGAATCACAGATTCAGGGTCAA
GCTTGAGACTTTTCTAGGCTGCCAGGA

Alignment

ORF - retro_cpor_283 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.24 %
• Parental protein coverage: 78.57 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SLGSNTYNRQNWEDADFPILCQTCLGENPYIRMTKEKYGKECKICARPFTVFRWCPGVRMRFKKTEVCQT
          SLGSN..NRQN.EDADF.ILCQ.CL.ENPY..M.KE.Y.KECKICARPFTVF..C..V.M.FKK..VC.T
Retrocopy SLGSNA*NRQNCEDADFLILCQICLCENPYLQMIKENYQKECKICARPFTVFHCCSEVCMCFKKI*VCLT

Parental  CSKLKNVCQTCLLDLEYGLPIQVRDAGLSFKDDMPKSDVNKEYYTQNME-REISNSDGTRPVGMLGKATS
          CSKLKN.CQ.CLLDLEYG.PIQV.D.GLSFKDD.P...VNKEYYTQNME.REISNSDG..PVG.LGKAT.
Retrocopy CSKLKNFCQLCLLDLEYGFPIQVSDSGLSFKDDIPMLYVNKEYYTQNME<REISNSDGISPVGTLGKATF

Parental  TSDMLLKLARTTPYYKRNR-PHICSFWVKGECKRGEECPYRHEKPTDPDDPLADQNIKDRYYGINDPVAD
          TSDMLLKLA.T..Y.KRN..PHICSFW.KGECKR.EECP..HEK.TD.D..LADQNIK..Y.G..DP.AD
Retrocopy TSDMLLKLAQTVSYSKRNH<PHICSFWLKGECKREEECP*IHEKLTDQDSSLADQNIKYWYCGMRDPEAD

Parental  KLL-KRASTMPRLDPPEDKTITTLYVGGLGDTITETDLRNHFYQFGEIRTITVVQRQQCAFIQFATRQAA
          KLL.K.AS....L.PP.DKT.TTLYV.GLG..ITET.LRNHFY..G.I.TITVVQRQQC.FI..ATRQAA
Retrocopy KLL>KQASAKLCLNPPKDKTFTTLYVIGLGSAITETYLRNHFYHLGVI*TITVVQRQQCTFI*LATRQAA

Parental  EVAAEKSFNKLIVNGRRLNVKWGRSQAARGKEKEKDGTTDSG-IKLEPVPG-LPG
          E.AAE..FN..IVNG.RL..KW.RSQAA.G.E.EKDG.TDSG..KLE...G.LPG
Retrocopy EMAAEETFN*PIVNGHRLSMKWARSQAAKGREREKDGITDSG<VKLETFLG<LPG

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	12.19 RPM
SRP017611_kidney	0.00 RPM	14.13 RPM
SRP017611_liver	0.00 RPM	9.45 RPM
SRP040447_lung	0.00 RPM	17.15 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.33 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_283 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_283 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 12 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000018082	1 retrocopy	retro_cfam_1480,
Callithrix jacchus	ENSCJAG00000020963	6 retrocopies	retro_cjac_1338, retro_cjac_2471, retro_cjac_3342, retro_cjac_3390, retro_cjac_3934, retro_cjac_990,
Cavia porcellus	ENSCPOG00000001946	2 retrocopies	retro_cpor_280, retro_cpor_283 ,
Dasypus novemcinctus	ENSDNOG00000011166	1 retrocopy	retro_dnov_2298,
Homo sapiens	ENSG00000086589	2 retrocopies	retro_hsap_3465, retro_hsap_4273,
Gorilla gorilla	ENSGGOG00000012947	2 retrocopies	retro_ggor_2337, retro_ggor_2859,
Myotis lucifugus	ENSMLUG00000009040	2 retrocopies	retro_mluc_1453, retro_mluc_153,
Macaca mulatta	ENSMMUG00000020683	4 retrocopies	retro_mmul_1199, retro_mmul_1348, retro_mmul_1553, retro_mmul_1762,
Monodelphis domestica	ENSMODG00000009574	1 retrocopy	retro_mdom_186,
Pongo abelii	ENSPPYG00000015955	4 retrocopies	retro_pabe_1412, retro_pabe_1594, retro_pabe_2861, retro_pabe_3486,
Pan troglodytes	ENSPTRG00000017423	2 retrocopies	retro_ptro_2348, retro_ptro_2898,
Tarsius syrichta	ENSTSYG00000003939	3 retrocopies	retro_tsyr_1090, retro_tsyr_1187, retro_tsyr_1231,