RetrogeneDB ID: retro_cpor_809

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_29:4820446..4821271(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM46
• Ensembl ID: ENSCPOG00000010284
• Aliases: None
• Description: None

Sequence

>retro_cpor_809
ATGAATGAAGACAATATGGATGGAACCAATGGATGCAGCAACATTTGAACTGGTATTCAGAATGAAGCGGCACTGCTTGC
TTTGATGGAGAAGCCTGGGTACAACTTGGTTCAAGAAAATGGACAAAGGAAATTCAGTGGTCCTCCTTCAGGCTGGGAAG
TTCCACCTTCATCTAGAAGATATGAAGTTTCTGTAGGAAAAATACCCTGCAATATTTATGAAGATGAGTTAGTTTCTGTA
TTTGAAAGAGCTGGGAAGATATATGAATTGCAACTTACGATGGAATTTAATGGTGAAAATAGGAGTTATGCTTTTGTGAT
GTATACTACAAAAGAAGAAGACCAGTTGGCTATCAGAATTCTTAATAATTATGAGATTCAACCAGGAAAGTTTATTGGTG
TTTGTGTGAGCTTGGGTGATTACAGATTATTTATTGGAGCTATTCCCAAGGAAAAGAAGAAAGAAGAAATTTTGGATGTA
ACGAAGAAAGTTACAGGAGTTGTAGATGCCATTGTTTATCCAAGTGCAATTGACAAGACCAAAAATCATGATTTTGCTTT
TGTTGAGTGTGAATCTCACAGAGCTGCTGCTATGGCTAGGAGAAAATTAATTCCAGGTGCCTTCCATCTGTGGGGCCATA
TTATTTAGATGGTTTGGGCTGATGCAGAGAAAGAACTTGAAGAGGAAACCATGCAAAGAGTTGAAGTTCTCTTTGTAAGA
AATTTAATAATCTCAACTACAGAGGAAACAAAGCACAATTTAGTAAATTCAAAGTAGGTGCTGTTGAAGGAGTCGAAAAA
TTTAAGAGATTATGCTTTTGTTCAC

Alignment

ORF - retro_cpor_809 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.98 %
• Parental protein coverage: 51.96 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNEENMDGTNGCSKVRTGIQNEAALLALMEKTGYNMVQENGQRKFGGPPPAGWEGPPPPRGCEVFVGKIP
          MNE.NMDGTNGCS...TGIQNEAALLALMEK.GYN.VQENGQRKF.GPP..GWE.PP..R..EV.VGKIP
Retrocopy MNEDNMDGTNGCSNI*TGIQNEAALLALMEKPGYNLVQENGQRKFSGPP-SGWEVPPSSRRYEVSVGKIP

Parental  RDMYEDELVPVFERAGKIYEFRLMMEFSGENRGYAFVMYTTKEEAQLAIRILNNYEIRPGKFIGVCVSLD
          ...YEDELV.VFERAGKIYE..L.MEF.GENR.YAFVMYTTKEE.QLAIRILNNYEI.PGKFIGVCVSL.
Retrocopy CNIYEDELVSVFERAGKIYELQLTMEFNGENRSYAFVMYTTKEEDQLAIRILNNYEIQPGKFIGVCVSLG

Parental  NCRLFIGAIPKEKKKEEILDEMKKVTEGVVDVIVYPSATDKTKNRGFAFVKYESHRAAAMARRKLIPGTF
          ..RLFIGAIPKEKKKEEILD..KKVT.GVVD.IVYPSA.DKTKN..FAFV..ESHRAAAMARRKLIPG.F
Retrocopy DYRLFIGAIPKEKKKEEILDVTKKVT-GVVDAIVYPSAIDKTKNHDFAFVECESHRAAAMARRKLIPGAF

Parental  QLWGHTIQVDWADPEKEVDEETMQRVKVLFVRNLMISTTEETIKAEFNKFKPGAVERVKKLRDYAFVH
          .LWGH.I...WAD.EKE..EETMQRV.VLFVRNL.ISTTEET.K......K.......K.LRDYAFVH
Retrocopy HLWGHII*MVWADAEKELEEETMQRVEVLFVRNLIISTTEET-KHNLVNSK*VLLKESKNLRDYAFVH

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	0.06 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.00 RPM	0.13 RPM
SRP040447_lung	0.00 RPM	0.15 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.03 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_809 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_809 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000010284	1 retrocopy	retro_cpor_809 ,
Tursiops truncatus	ENSTTRG00000001239	1 retrocopy	retro_ttru_1228,