RetrogeneDB ID: retro_cpor_683

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_23:11826255..11827306(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000027613
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RBM48
• Ensembl ID: ENSCPOG00000007376
• Aliases: None
• Description: None

Sequence

>retro_cpor_683
GACCACCACGTCCAGAGGGCAGTTTGAGACACAAGGGCGAAATATTGAGAGGGCCAACTGCCTCATGCGGTCAAGGTCTA
TACAATCAATTTGGAATCCCAGTACTCACTGATGCAAGGAGTTCCTGCAGTGGGAGCAATGAAGGAATTAGTTGAGCGAT
TTGCCCTTTATGGCACAACTGAAGAGTGTAATGCTCTAGATGAATATCTAGCAGAAGACTTTGCGGAAGTTTATCTTACT
AAGTTTATGAATTTACAAAATGCAAGGATAGCCAAGAGAAAAATGGATGAGCAGAGTTTCTTTGGTGGATTGCTTCATGT
TTGCTATGCTCCAGAATTCGAGACAGTTGAAGAAACTAGAAAAAAATTAGAAGAAAGAAAGGCTAATATAGCACGAACTA
TTAAAAATAAAGACTATTATATGGCTAAGAAGAAACTGGTTCCAGAGCTTAAAGATACAGAAGATTTTAGACAGGCCCTA
TACTCAGATGTGTCTGGATTTTATGTAGCTTTGAACACACCTCCTGGGATCCAAGATCCTTGGTTTCCTTATTCTTGTGA
ATTGCCTTTATGTTATTTTGCCTTAAAACCTGCATGTTCACCTAGGGAGCATGTAGACAGAGCATTGGAGGTCTATAAAG
ATGGTAGAGACCATAATGAAGCAATGAAACACTGTATCCACAGCAACTCTTCACTCCTAACACAGATGACCACTTCTAAA
AATTCCTGTTCTGGAGCCCAAAAAAGCCATTACTCCTTCAGGGGAATTGACAGATTTATGTCTAGGACAACACAGTTGCA
GGAGCGGAAAAGAAGAGAAGATGATTGCAAACTTGAAACTTTTGAAGCAAGCACAAGCAGTAATGAGATCATGTTTGGGC
CTAAGTTACCAGACATACCTAAAGTGGATCTGCAAGACGATTCCTTGAATACATCAGCAAACTTAATTCGGAATAAACTT
AAAAGAGTTAATTTCATCTGTGCCAAAGCATCCAGAGGACAAATTGGAAGCTGTTTGTACCAGTCATCCATTAAAACAAA
GAAGAAGAATA

Alignment

ORF - retro_cpor_683 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.68 %
• Parental protein coverage: 96.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DHHVQRAVCDTRAKYREGRRPRAVKVYTINLESRYLLVQGVPAVGAMKELVERFALYGTIEEYNALDEYP
          DHHVQRAV.DTRAKY.EG..P.AVKVYTINLES.Y.L.QGVPAVGAMKELVERFALYGT.EE.NALDEY.
Retrocopy DHHVQRAV*DTRAKY*EGQLPHAVKVYTINLESQYSLMQGVPAVGAMKELVERFALYGTTEECNALDEYL

Parental  AEDFTEVYLIKFMNLQNARIAKRKMDEQSFFGGLLHVCYAPEFETVEETRKKLEERKAYIARTTKNKEKD
          AEDF.EVYL.KFMNLQNARIAKRKMDEQSFFGGLLHVCYAPEFETVEETRKKLEERKA.IART.KN..KD
Retrocopy AEDFAEVYLTKFMNLQNARIAKRKMDEQSFFGGLLHVCYAPEFETVEETRKKLEERKANIARTIKN--KD

Parental  YYMTKKKLVPEHKDTEDFRQALYSDVSGFYAATLNTPPGIQNPQFPYSCELPLCYFASKPACSLGEHVDR
          YYM.KKKLVPE.KDTEDFRQALYSDVSGFY.A.LNTPPGIQ.P.FPYSCELPLCYFA.KPACS..EHVDR
Retrocopy YYMAKKKLVPELKDTEDFRQALYSDVSGFYVA-LNTPPGIQDPWFPYSCELPLCYFALKPACSPREHVDR

Parental  ASDVYKDGRDHSEAMKHCIHSDSSLQTQITTSKNSCSGAQ-KAINPSG-AIDRFMPRTTQLQERKRRRED
          A..VYKDGRDH.EAMKHCIHS.SSL.TQ.TTSKNSCSGAQ.KAI.PSG..IDRFM.RTTQLQERK.RRED
Retrocopy ALEVYKDGRDHNEAMKHCIHSNSSLLTQMTTSKNSCSGAQ>KAITPSG<GIDRFMSRTTQLQERK-RRED

Parental  DRKLETFEASTSSNEVMIGPKLPDIPKVDLQDDSLNTSANLIRNK-LKEVISSVPKHPEDKLKAVCTSHP
          D.KLETFEASTSSNE.M.GPKLPDIPKVDLQDDSLNTSANLIRNK.LKE.ISSVPKHPEDKL.AVCTSHP
Retrocopy DCKLETFEASTSSNEIMFGPKLPDIPKVDLQDDSLNTSANLIRNK>LKELISSVPKHPEDKLEAVCTSHP

Parental  LKQRRRI
          LKQRRRI
Retrocopy LKQRRRI

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	9.55 RPM
SRP017611_kidney	0.00 RPM	12.25 RPM
SRP017611_liver	0.00 RPM	6.79 RPM
SRP040447_lung	0.00 RPM	9.61 RPM
SRP040447_skeletal_muscle	0.00 RPM	5.72 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_683 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_683 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	ENSCPOG00000007376	1 retrocopy	retro_cpor_683 ,
Dipodomys ordii	ENSDORG00000005900	1 retrocopy	retro_dord_71,