RetrogeneDB ID: retro_cpor_778

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_27:20224765..20225463(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBMXL1
• Ensembl ID: ENSCPOG00000012164
• Aliases: None
• Description: None

Sequence

>retro_cpor_778
GAAACAAATGAGAAAGCCCTTCCAGCGGTATTTGGAAAATATAACAGACAGTGGAAATACTGTTCTTGATGAAGACCAAG
AAACCAGTAAATCAAGAGGATTTGCTCTTGTTACCTTGAAAGCCCAACAGATGCTAAGGATGCAGCTAGGGACAAGAATG
GAAAGTCCTCAGATGGAAAAGCCATCAACGTGGAACAAGCCACCAAACCATCATTTGAAAGTGGAAGACAAGGACCACCT
CCACCTCCGAGCAGCAGAGGCGCTCCCAGAGGTCTTAGAGGAGGAAGTGGAGGCACAGGGGCCCTCCCTCACTGGAGGGC
ACATGGAGGATGGTGGCTATCCCATGAATTTTAACATAAATTCTTCCAGGGGGCCCTGCCAGTGAAAACAGGATCTCCAC
CACAAAGCAGGAGTCCTCCTCCTAAAAGGTCAGCCCCATCAGGACCAGCTCTCAGCAGCAGTGGAATGGGAGAAAGAGCC
CCTCTATCATGGAGAAGAGATAGTTATGGGGGCCTGCCTCGAAGGGAACTCCTGCCCTCTCCTAGAATGTTTATTTGCCT
CCAAAAGATGATGAATATTTGACTAAAGACAGCTATCAAAGCTGACATTACCCAAGTTCTCGCGATACAAGAGATCAGGC
CCCACTACCAAGAGAGGATACTTATCAGGATTTCAGTTATTCCAGTTCACGTGATGAC

Alignment

ORF - retro_cpor_778 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.1 %
• Parental protein coverage: 60.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  ETNEKALEAVFGKYGR-IVEVL-LMK-DRETNKSRGFAFVTF-ESPADAKDAARDMNGKSLDGKAIKVEQ
          ETNEKAL.AVFGKY.R..VE.L.LMK.D.ET.KSRGFA.VT..ESP.DAKDAARD.NGKS.DGKAI.VEQ
Retrocopy ETNEKALPAVFGKYNR<TVEILFLMK<DQETSKSRGFALVTL<ESPTDAKDAARDKNGKSSDGKAINVEQ

Parental  ATKPSFESGRRGPPPPPRSRGPPRGLRGGRGGSGGT-RGPPS-HGGHMDDGGYSMNFNMSSSRGP-LPVK
          ATKPSFESGR.GPPPPP.SRG.PRGL...RGGSGGT.RGPPS..GGHM.DGGY.MNFN..SSRGP.LPVK
Retrocopy ATKPSFESGRQGPPPPPSSRGAPRGL---RGGSGGT<RGPPS<TGGHMEDGGYPMNFNINSSRGP<LPVK

Parental  RGPPPRSGGPPPKRSAPSGPVRSSSGMGGRAPVSRGRDSYGGPPRREPLPSRR-DVYLSPRDDGYSTKDS
          .G.PP.S..PPPKRSAPSGP..SSSGMG.RAP.S..RDSYGG.PRRE.LPS.R..VYL.P.DD.Y.TKDS
Retrocopy TGSPPQSRSPPPKRSAPSGPALSSSGMGERAPLSWRRDSYGGLPRRELLPSPR<NVYLPPKDDEYLTKDS

Parental  YSSRDYPSSRDTRDYAPPPRDYTYRDYGHSSSRDD
          Y.S..YPSSRDTRD.AP.PR..TY.D...SSSRDD
Retrocopy YQS*HYPSSRDTRDQAPLPREDTYQDFSYSSSRDD

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	63.90 RPM
SRP017611_kidney	0.00 RPM	67.52 RPM
SRP017611_liver	0.00 RPM	33.25 RPM
SRP040447_lung	0.00 RPM	95.39 RPM
SRP040447_skeletal_muscle	0.01 RPM	35.60 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_778 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_778 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 20 parental genes, and 43 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013308	1 retrocopy	retro_btau_36,
Canis familiaris	ENSCAFG00000018962	4 retrocopies	retro_cfam_1106, retro_cfam_1244, retro_cfam_1649, retro_cfam_1914,
Choloepus hoffmanni	ENSCHOG00000012369	3 retrocopies	retro_chof_1240, retro_chof_2596, retro_chof_880,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Cavia porcellus	ENSCPOG00000006313	1 retrocopy	retro_cpor_162,
Cavia porcellus	ENSCPOG00000012164	1 retrocopy	retro_cpor_778 ,
Felis catus	ENSFCAG00000004779	1 retrocopy	retro_fcat_1903,
Homo sapiens	ENSG00000147274	7 retrocopies	retro_hsap_23, retro_hsap_3074, retro_hsap_3587, retro_hsap_4144, retro_hsap_4846, retro_hsap_800, retro_hsap_91,
Gorilla gorilla	ENSGGOG00000006944	1 retrocopy	retro_ggor_657,
Loxodonta africana	ENSLAFG00000005568	3 retrocopies	retro_lafr_1188, retro_lafr_276, retro_lafr_35,
Microcebus murinus	ENSMICG00000006856	2 retrocopies	retro_mmur_1252, retro_mmur_661,
Myotis lucifugus	ENSMLUG00000013209	5 retrocopies	retro_mluc_1630, retro_mluc_1746, retro_mluc_203, retro_mluc_2180, retro_mluc_80,
Mustela putorius furo	ENSMPUG00000001855	2 retrocopies	retro_mputfur_1539, retro_mputfur_956,
Mus musculus	ENSMUSG00000031134	2 retrocopies	retro_mmus_170, retro_mmus_187,
Oryctolagus cuniculus	ENSOCUG00000007220	1 retrocopy	retro_ocun_3,
Pongo abelii	ENSPPYG00000020771	3 retrocopies	retro_pabe_2548, retro_pabe_303, retro_pabe_766,
Rattus norvegicus	ENSRNOG00000000866	1 retrocopy	retro_rnor_268,
Ictidomys tridecemlineatus	ENSSTOG00000006211	2 retrocopies	retro_itri_1205, retro_itri_1346,
Tupaia belangeri	ENSTBEG00000001154	1 retrocopy	retro_tbel_1919,
Tursiops truncatus	ENSTTRG00000007322	1 retrocopy	retro_ttru_1450,