RetrogeneDB ID: retro_cpor_237

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_107:75651..76218(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM18
• Ensembl ID: ENSCPOG00000013811
• Aliases: None
• Description: None

Sequence

>retro_cpor_237
GTGGAAACAGAAACCAAAACTCTTCCCCTGGAGAATGCATCCATCCTTTCAGAAGGTTCTCTAAAGTAAGGACACCAACT
ATGGATTGGCAATGTGGACCCCAAAATCACAGAATACCAGCTCCTCAAGCTCCTCCAGAAGTTTGGGAAGATGAAGCAGT
ATGACTTCCTCTTCCGCCAAGTCAGGTGTTTTGGAAGAACAGCCTCAAGGTTACTGCTTCGTTAACTGTGAAACTAAGCA
GGAAGCAGAGCAAGCCATTCAGTGTTTCAATGGCAAACTGGCACTAAGAAGCTTGTGATACGACGGTTCCATGCCCAAAT
AAAGAGGTAGGATCCTGATAAGAATGGTAGCATTGTTCCAATCAGTCTCGAGCCATCTTCAAGCACTGAGCCTATGCAGT
CTAACCTAAGTGTCACTGCAAAGATGAAAGCCATTGAAGCAAAGCTGAAAATGATGGCACAAAATTGTGATGTGAAATAC
CCAGCAGCGCCTGTTTTTTTCCTACTTTAAACCACCAGATACAATAGGACTCCCCCTTATTCTAGAACAGCGTGGAAATC
TTGAAGA

Alignment

ORF - retro_cpor_237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.84 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MEAETKTLPLENASILSEGSLQEGHRLWIGNLDPKITEYHLLKLLQKFGKVKQFDFLFH-KSGALEGQPR
          .E.ETKTLPLENASILSEGSL..GH.LWIGN.DPKITEY.LLKLLQKFGK.KQ.DFLF..KSG.LE.QP.
Retrocopy VETETKTLPLENASILSEGSLK*GHQLWIGNVDPKITEYQLLKLLQKFGKMKQYDFLFR>KSGVLEEQPQ

Parental  GYCFVNFETKQEAEQAIQCLNGKLAL-SKKLVVRWAHAQIKRYDHNKNDKILPISLEPSSSTEPTQSNLS
          GYCFVN.ETKQEAEQAIQC.NGKLAL..K....R..HAQIKR.D..KN..I.PISLEPSSSTEP.QSNLS
Retrocopy GYCFVNCETKQEAEQAIQCFNGKLAL<KKLVIRRF-HAQIKR*DPDKNGSIVPISLEPSSSTEPMQSNLS

Parental  VTAKIKAIEAKLKMMAENPDAEYPAAPV-YSYFKPPDK-KRTNPYSRTAWKSRR
          VTAK.KAIEAKLKMMA.N.D..YPAAPV..SYFKPPD...RT.PYSRTAWKS.R
Retrocopy VTAKMKAIEAKLKMMAQNCDVKYPAAPV>FSYFKPPDT<NRTPPYSRTAWKS*R

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	14.09 RPM
SRP017611_kidney	0.00 RPM	11.10 RPM
SRP017611_liver	0.00 RPM	5.75 RPM
SRP040447_lung	0.00 RPM	13.67 RPM
SRP040447_skeletal_muscle	0.00 RPM	20.26 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_237 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_237 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013811	1 retrocopy	retro_cpor_237 ,
Myotis lucifugus	ENSMLUG00000004794	1 retrocopy	retro_mluc_298,
Monodelphis domestica	ENSMODG00000019688	1 retrocopy	retro_mdom_1462,
Oryctolagus cuniculus	ENSOCUG00000008527	1 retrocopy	retro_ocun_290,
Otolemur garnettii	ENSOGAG00000015104	1 retrocopy	retro_ogar_846,
Ochotona princeps	ENSOPRG00000010381	2 retrocopies	retro_opri_1123, retro_opri_360,
Ictidomys tridecemlineatus	ENSSTOG00000022388	1 retrocopy	retro_itri_1882,
Tupaia belangeri	ENSTBEG00000016520	1 retrocopy	retro_tbel_2898,