RetrogeneDB ID: retro_cpor_911

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_33:20728607..20729174(+)
• Located in intron of: ENSCPOG00000005571

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBFA
• Ensembl ID: ENSCPOG00000000170
• Aliases: None
• Description: None

Sequence

>retro_cpor_911
ACACAGAGGCCGTTCTACAGGAGTGCTGGATACATGAGGTACCTTTTGATGGCCCAGCAGACACTCAGAAATGTGCCACC
AAGAGTGTTTGTTCAAGACAGAAGAAACGCACTTCTGGCTGAGGTTCATCAGTTGCTGGCAGTAGCTGACATGGATGAAA
TAGACAACTTGGCACAAGATCATTTCAGGGACCCTGATGCCCTGTCACCACATGACCCCCCAGGACCTGCTGCACATGGT
TATCTCTGTAGGATTGATCACAATGCACTCAACAAACAAATAATGGAATACAAATGGAAGAAGGAAAAAGGACTCCAGGA
CATGAGCCCGGTCTCGCCTGGGCAAATGCAAATCGGTAAGCTGCCACAGTGGGTGAGGAGGAGAAGGAAAGCCCTATCAC
AGGCAGACCAGGACACCTCCCCCAGGAGTTTCCTCTTGGGTGAGGAGAGTAAGGATAAGGATGAGGACAGTATCCTGGAG
TGTGGATCCCAGAACGCAGAGAAGTAGGAGGCAGAACGTGGAGGTAGGGGGACACAGCAGGACCCCCATGGCAGAACAGA
GCAAGGA

Alignment

ORF - retro_cpor_911 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.51 %
• Parental protein coverage: 55.65 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TEAVLQRSAGYMRHLLMAQQTLRNVPPIVFVQDRRNALLAEVDQLLAVADFGPMDETDNLAQA--RDPDA
          T.....RSAGYMR.LLMAQQTLRNVPP.VFVQDRRNALLAEV.QLLAVAD...MDE.DNLAQ...RDPDA
Retrocopy TQRPFYRSAGYMRYLLMAQQTLRNVPPRVFVQDRRNALLAEVHQLLAVAD---MDEIDNLAQDHFRDPDA

Parental  LSPHDPPGPAAHGYLCGIDHNALNKQIMEYKRKKEKGLQDTRVVSPGQVQMAKVPQWVRRRRKALSQADQ
          LSPHDPPGPAAHGYLC.IDHNALNKQIMEYK.KKEKGLQD...VSPGQ.Q..K.PQWVRRRRKALSQADQ
Retrocopy LSPHDPPGPAAHGYLCRIDHNALNKQIMEYKWKKEKGLQDMSPVSPGQMQIGKLPQWVRRRRKALSQADQ

Parental  DTSPRSFLLGEDSEDKDEDSILECGCQSQNTEEWEAEPGGRGTQQDPHGRTEQG
          DTSPRSFLLGE.S.DKDEDSILECG..SQN.E..EAE.GGRGTQQDPHGRTEQG
Retrocopy DTSPRSFLLGEESKDKDEDSILECG--SQNAEK*EAERGGRGTQQDPHGRTEQG

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	0.35 RPM	25.65 RPM
SRP017611_kidney	1.05 RPM	37.79 RPM
SRP017611_liver	0.52 RPM	26.29 RPM
SRP040447_lung	0.03 RPM	35.81 RPM
SRP040447_skeletal_muscle	0.09 RPM	35.56 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_911 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_911 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000036297	1 retrocopy	retro_btau_1031,
Cavia porcellus	ENSCPOG00000000170	1 retrocopy	retro_cpor_911 ,
Equus caballus	ENSECAG00000008292	1 retrocopy	retro_ecab_146,
Pan troglodytes	ENSPTRG00000010137	1 retrocopy	retro_ptro_1062,