RetrogeneDB ID: retro_cpor_1246

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_6:17533273..17534474(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000022840
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: QRICH1
• Ensembl ID: ENSCPOG00000009958
• Aliases: None
• Description: None

Sequence

>retro_cpor_1246
GTAGTGCAGACCCTTGCATACTCTCTCTTTCCAGCACAGTTTATGAATGGCAACATCCACATTCCAGTAGCTGTGCAGGC
TGTGGCAGGCACATACCAGAATACAGCTCCGACTGTCCATATACGGGGCACCCAGCAGCAGCCACAACAACAGACCCCCC
CCAAGAACAGACACCATCACCACCACAGCAGCAGCAGCAGCAGCTCCTGGTTATTTGTCCAGCTCAGACTGTCCAAGTTG
CTAAAGTTGAACCAAAGTCACAGCCACAGCCTTCCCCAGAACTTCTGCTTCCAAATTCTTTGAAACCAGAAGAAGGGCTT
GAAGTATGGAAAAACTGGGCCTAGACCAAGAATGGTGAACTGGAGAAGGATGCTCAGAACAGATTGGCTCCCATTGGGAG
GCACCAACTGCTTCGATTCCAAGATCTTATCTCCTCTGCTGTGGTTGAGTTGAATTATGGGCTGTGTCTAATGACATGGG
AAGCTTGAAATGGAGACTGTGAACCCTATGATCCTGATGTGCTGTACTATATTTTCCTGTGTATTCAAAAGTATCTTTTT
GAAAACGGAAGGGTGGATGACATTTTCTCTGATCTTTACTGTGTTTGATTCACGGAGTGGCTACATGAAATTCTGAAGGA
TGTTTAACCCCAGGTCACTCCACTTGGCTATGTCTTGCCCAGCCAGGTGACTGAGGAGATGCTGTGGGAGTGCAAGCAAC
TTGGGGCACACTTCCCCTCAACCCTACTGACCACCCTCATGTTCTTTAATCCCAAGTACTTCCTGTTGAAGACAGTGGCC
AGCACATGAAACTGGCCTTCTCTAAGGCCTTACGACAGACAAAGAAGAACCCCTCTAATCCCAAGGATAAAAACACGAGT
ATCTGGTACCTGAAGGCCCTTAGAATACATCAGACTGGCCAGAAAGTTTCAGATGACATGTATGCGGAGCAGACAGAAAA
TCCAGAGAATCCATTGAGGTGTCCCATCAAGCTCTATGATTTCTACCTCTTCAAATGTCCCCAGAGTGTGAAAGGCCAGA
ATGACACCTTTTACCTGACACCTGAGCCAGTAGTGGCCCCCAGCAGCCCAATCTGGTACTCAGTCCAGCCTATCACCCGA
GAGCAGATGGGACAAATGCTGACCCGAATCCTGGAGATACGAGAAATTCAGGAGGCCATTGCAGTGGCCAGCGCAAGCAC
A

Alignment

ORF - retro_cpor_1246 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.88 %
• Parental protein coverage: 51.54 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VVQTLANSLFPAQFMNGNIHIPVAVQAVAGTYQNTAQTVHIWDPQQQP-QQQTPQ-EQTPPPPQQQQQQL
          VVQTLA.SLFPAQFMNGNIHIPVAVQAVAGTYQNTA.TVHI...QQQP.QQ.....EQTP.PP.......
Retrocopy VVQTLAYSLFPAQFMNGNIHIPVAVQAVAGTYQNTAPTVHIRGTQQQPQQQXXXK<EQTPSPPXXXXXXX

Parental  QVTCSAQTVQVAEVEPQSQPQPSPELLLPNSLKPEEGLEVWKNWAQTKNAELEKDAQNRLAPIGRRQLLR
          .V.C.AQTVQVA.VEP.SQPQPSPELLLPNSLKPEEGLEVWKNWA.TKN.ELEKDAQNRLAPIGR.QLLR
Retrocopy LVICPAQTVQVAKVEPKSQPQPSPELLLPNSLKPEEGLEVWKNWA*TKNGELEKDAQNRLAPIGRHQLLR

Parental  FQEDLISSAVAELNYGLCLMTREARNGEGEPYDPDVLYYIFLCIQKYLFENGRVDDIFSDLYYVRFTEWL
          FQ.DLISSAV.ELNYGLCLMT.EA.NG..EPYDPDVLYYIFLCIQKYLFENGRVDDIFSDLY.V.FTEWL
Retrocopy FQ-DLISSAVVELNYGLCLMTWEA*NGDCEPYDPDVLYYIFLCIQKYLFENGRVDDIFSDLYCV*FTEWL

Parental  HEVLKDVQPRVTPLGYVLPSHVTEEMLWECKQLGAHSPSTLLTTLMFFNTKYFLLKTV-DQHMKLAFSKV
          HE.LKDV.P.VTPLGYVLPS.VTEEMLWECKQLGAH.PSTLLTTLMFFN.KYFLLKTV..QHMKLAFSK.
Retrocopy HEILKDV*PQVTPLGYVLPSQVTEEMLWECKQLGAHFPSTLLTTLMFFNPKYFLLKTV<GQHMKLAFSKA

Parental  LRQTKKNPSNPKDKSTSIRYLKALGIHQTGQKVTDDMYAEQTENPENPLRCPIKLYDFYLFKCPQSVKGR
          LRQTKKNPSNPKDK.TSI.YLKAL.IHQTGQKV.DDMYAEQTENPENPLRCPIKLYDFYLFKCPQSVKG.
Retrocopy LRQTKKNPSNPKDKNTSIWYLKALRIHQTGQKVSDDMYAEQTENPENPLRCPIKLYDFYLFKCPQSVKGQ

Parental  NDTFYLTPEPVVAPNSPIWYSVQPISREQMGQMLTRILVIREIQETIAVASAST
          NDTFYLTPEPVVAP.SPIWYSVQPI.REQMGQMLTRIL.IREIQE.IAVASAST
Retrocopy NDTFYLTPEPVVAPSSPIWYSVQPITREQMGQMLTRILEIREIQEAIAVASAST

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	47.22 RPM
SRP017611_kidney	0.00 RPM	40.83 RPM
SRP017611_liver	0.00 RPM	30.03 RPM
SRP040447_lung	0.00 RPM	54.78 RPM
SRP040447_skeletal_muscle	0.00 RPM	25.32 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1246 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1246 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	ENSCPOG00000009958	1 retrocopy	retro_cpor_1246 ,