RetrogeneDB ID: retro_cpor_1066

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_43:568454..569585(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000010178
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PJA2
• Ensembl ID: ENSCPOG00000014595
• Aliases: None
• Description: None

Sequence

>retro_cpor_1066
TTTAATAGGCATGAAACTAAACAGAAAACTGTTCAGAGATGGAGGGAGGCTTTGGAAGTTGAGGAATGTGGCTCAGATGA
CCGCTTAATAAAATGTGAAGAATATGATGATGGAGAGCATGACTGTATATTCTTGGATCTTCCTTATGCAAGAGTCACAC
CACAGGAAACAGAAAACCATATAACATCTGAAAATAGAGCTGCAGCAGGAAAGCAAGAAGTTCGGGACAGTGCCTTTTGG
AATGGCTGCAGAGATTATTACCAGCTCTTTGACAGAGATGAAGATAGTTCAGAATGTAGTGATGGGGAGTGGTCCTGCTT
CTTTGCCTCATCGATTTTCTGGTTCAGAAAAAGATCAGTCCTCAAGTGATGAAAGCTGGAGACTCTGCCAGGAAAAGATA
AGAATGAACCTGAGCTGCAGAGTGATAGCAGTGGCCCCGAAGAAGAAAACCAAGAATTATCTCTGCAGGAAGGGGAGCAG
ACATCCTTGGAAGAGGGAGAGATTCCTTGGCCGCGGTACAGTGAAGTCAATGAAAGCAGCAATGATGAGGGAAATGAGCC
CGCCAATGAATTTCCACAGCCAGAAGCTTTCATGTTGGACAGTAACAACAATCTTGAGGATGACTCCAGTGTGAGTGAAA
ACTTGGATGTGGATTGGAGTTTATTTGACGGCTTTGCAGATGGCCTTGGAGTTGCTGAAGCTATTTCTTATGTGGATCCT
CAGTTCCTCACCTGCATGGCACTGGAAGAGCGCTTAGCCCAGGCTATGAAGACTGCACTGGCACATTTAGAGTCCCTGGC
AGTGGATGTGGAGGTGGCCAATCCACCAGCCAGTAAGGAGAGCATCGATGTCCTGCCAGAGACCCTTGTTCTTGAAGATC
ACACTGCTATTGGTCAGGAGCAGTGCTGTCCAATCTGTTGCAGTGAATATATAAAGAATGATATAGCAACAGAGTTACCC
TGTCACTGTTTCTTTCACAAACCTTGCGTCTCAATTTGGCTACAGAAGTCGGGAACATGCCCTGTGTGCTGCTGCCATTT
CCCACCTGCAGTTATTGAAACGTCTGCAGCTGGTTCCTCTGAGTTTGAGCCTGATGCCCCACCTTCAACTGACAGCACTG
CAGAAGCCCCC

Alignment

ORF - retro_cpor_1066 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.14 %
• Parental protein coverage: 53.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FNRHEAKQRSVQRWREALEVEECASDDPLIKCEEYDDGEHDCMFLDLPYARVTPQETENHITSESRAAAG
          FNRHE.KQ..VQRWREALEVEEC.SDD.LIKCEEYDDGEHDC.FLDLPYARVTPQETENHITSE.RAAAG
Retrocopy FNRHETKQKTVQRWREALEVEECGSDDRLIKCEEYDDGEHDCIFLDLPYARVTPQETENHITSENRAAAG

Parental  RQEVRDSAFWNGCRDYYQLFDRDEDSSECSDGEWS-ASLPHRFSGSEKDQSSSDESW-ETLPGKDENEPE
          .QEVRDSAFWNGCRDYYQLFDRDEDSSECSDGEWS.ASLPHRFSGSEKDQSSSDESW.ETLPGKD.NEPE
Retrocopy KQEVRDSAFWNGCRDYYQLFDRDEDSSECSDGEWS>ASLPHRFSGSEKDQSSSDESW<ETLPGKDKNEPE

Parental  LQSDSSGPEEENQELSLQEGEQTSLEEGEIPWLQYSEVNESSSDEGNEPANEFAQPEAFMLDGNNNLEDD
          LQSDSSGPEEENQELSLQEGEQTSLEEGEIPW..YSEVNESS.DEGNEPANEF.QPEAFMLD.NNNLEDD
Retrocopy LQSDSSGPEEENQELSLQEGEQTSLEEGEIPWPRYSEVNESSNDEGNEPANEFPQPEAFMLDSNNNLEDD

Parental  SSVSEDLDVDWSLFDGFADGLGVAEAISYVDPQFLTYMALEERLAQAMETALAHLESLAVDVEVANPPAS
          SSVSE.LDVDWSLFDGFADGLGVAEAISYVDPQFLT.MALEERLAQAM.TALAHLESLAVDVEVANPPAS
Retrocopy SSVSENLDVDWSLFDGFADGLGVAEAISYVDPQFLTCMALEERLAQAMKTALAHLESLAVDVEVANPPAS

Parental  KESIDGLPETLVLEDHTAIGQEQCCPICCSEYIKDDIATELPCHHFFHKPCVSIWLQKSGTCPVCRRHFP
          KESID.LPETLVLEDHTAIGQEQCCPICCSEYIK.DIATELPCH.FFHKPCVSIWLQKSGTCPVC..HFP
Retrocopy KESIDVLPETLVLEDHTAIGQEQCCPICCSEYIKNDIATELPCHCFFHKPCVSIWLQKSGTCPVCCCHFP

Parental  PAVIEASAAGSSELEPDAPPSTDSTAEAP
          PAVIE.SAAGSSE.EPDAPPSTDSTAEAP
Retrocopy PAVIETSAAGSSEFEPDAPPSTDSTAEAP

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	0.12 RPM	290.80 RPM
SRP017611_kidney	0.00 RPM	92.75 RPM
SRP017611_liver	0.00 RPM	63.72 RPM
SRP040447_lung	0.00 RPM	74.45 RPM
SRP040447_skeletal_muscle	0.03 RPM	38.24 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1066 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1066 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014595	1 retrocopy	retro_cpor_1066 ,