RetrogeneDB ID: retro_cpor_454

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:28754763..28756070(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MSR1
• Ensembl ID: ENSCPOG00000022785
• Aliases: None
• Description: None

Sequence

>retro_cpor_454
GTAAGAGAAGGCAGTATGGAGCAGCAGAATGTCTTTCTTGATCACCAGGAGGAGCCTGATAGCTCTTCAGATTCTGTGTA
ATTTGATGCTTGTTTAATAACAGCACTGCTTCCTCCCAATCCTAAAAATGGCCACCGAGAGAAACTGAAGTCCTTCAAAG
CTGCACTCATTGCCCTGTATCTCCTTGCACTTGTCACCCTGATACCTGTCATCAGCATAGTGGCAGCTCATCTTCTGAAG
TGGGAAGTGAAGAATTGCATGGTTGGTTCAGCTCATGCAAATGCTATGTCTCAAAGTCTTGGAAAATGAATGACAGTGAA
GATGCAATGAGATTTCCAGAAATTGTTTTGGGACACATCAACAACACTGAGAAAAAATACAGTACATTTCAGATGCAGAA
GCCAATTTCATAGGTTCAGAACACTTCCAAAATTTCAGTGTGACAACTGATCAAAGATTCAGTTATGCTTTTCTGCAGCT
AAGTACCTTAGTATCCTCAATCCAAGAACATAAGAACACAATACATGAGATCTCCAAACCCTTAGTAAGTCTGAATAGCA
CATTCCTTGATCTGCAGCTCAATATAGGAACATTGAATTTTTTAAAAGTCCAGGAGACTAAATTGAAGCAACACGAGGAT
ATTAGTAAATTGAAGGAGCATTATACAATGCATCAACAGAAATTAAGTCGCTAAAAGAGCAAGAGCATGTGGAAGGGGAA
TAAAGAAAGAGTTGAAAGTGCTGAAGAATATCACCAGTGATCTTAGCTTGAAAGATTGCAACCATTCTCTGAAATTGAAA
AATACAACTTTAATTCAAGGTTTCCCTGGACCCAGAGGTGAAAAAGGAGACAGAGATCCCACTGAAGAAATTGATATACC
AGGCATTCCAGGTCTAAGAGATCGTCCAGGTCTTAAAGGTGATACAGAAGGAGCTGGCTTTCCTGGAAGTAGAGGCTACT
TGGGACCAACAGGAAATGTGGGAAGGCCAGGAAATCCTGGACAAAAAGGTCAAAAAGGAGCAAAAGGAAGAAGGAGCATA
TTCCCTCTGCCAAGACAGTTCGACTGGCTAATGGTAAAGGCCACAGAAGGGTAGAAGGACATTTTCCAGGAGGGCCGTTA
GAGCACCATTTGGGATGATCGCTGGGAAATACAAGTTGCATCTGTCATCTGGTGAAGTTTGGAATACAAAGGTGTTCAAG
CTGTGCACAAAGTAGCTTATTTTGGACAAGGTACTGGTCCAATATGGTTGACTGAAGTATTTTGTTTTGGGAGAAAATTA
TCTATGGAGAAATGTAATATCAGGCAA

Alignment

ORF - retro_cpor_454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.4 %
• Parental protein coverage: 96.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  VFDSIMESRNIFLDHQEELDIYSDSVKFDARSMTALLPPNPKNGLQEKLKSFKAALIALYLLVFVVLIPV
          V....ME..N.FLDHQEE.D..SDSV.FDA...TALLPPNPKNG..EKLKSFKAALIALYLL..V.LIPV
Retrocopy VREGSMEQQNVFLDHQEEPDSSSDSV*FDACLITALLPPNPKNGHREKLKSFKAALIALYLLALVTLIPV

Parental  ISIVAAHLLKREMKNCTVGSPHASAMSQSLGK-GNGSEDAMKFQEFVLEHISNIERR-IQDISDAEASFI
          ISIVAAHLLK.E.KNC.VGS.HA.AMSQSLGK..N.SEDAM.F.E.VL.HI.N.E...IQ.ISDAEA.FI
Retrocopy ISIVAAHLLKWEVKNCMVGSAHANAMSQSLGK<MNDSEDAMRFPEIVLGHINNTEKK<IQYISDAEANFI

Parental  GSENFQNFSMTTDQRLNSVFLQLNNLVSSVQEHESAVDEISKSLVSLNTTLLDLQLSIETLN-KKVQETT
          GSE.FQNFS.TTDQR....FLQL..LVSS.QEH.....EISK.LVSLN.T.LDLQL.I.TLN..KVQET.
Retrocopy GSEHFQNFSVTTDQRFSYAFLQLSTLVSSIQEHKNTIHEISKPLVSLNSTFLDLQLNIGTLNFLKVQETK

Parental  LKQQEDISKLKEH-VYNASAEIKSLKEEQEHIEEE-IKKELKVLNNVTNDLRLKDWEHSLTLRNITLIQG
          LKQ.EDISKLKEH..YNAS.EIKSLKE.QEH.E.E.IKKELKVL.N.T.DL.LKD..HSL.L.N.TLIQG
Retrocopy LKQHEDISKLKEH<LYNASTEIKSLKE-QEHVEGE<IKKELKVLKNITSDLSLKDCNHSLKLKNTTLIQG

Parental  PPGPRGEKGDRGAPGQTGIPGLPGLRGPPGLKGDRGVTGFPGSKGYPGPAGNVGRPGNPGQKGQKGEKGT
          .PGPRGEKGDR.......IPG.PGLR..PGLKGD....GFPGS.GY.GP.GNVGRPGNPGQKGQKG.KG.
Retrocopy FPGPRGEKGDRDPTEEIDIPGIPGLRDRPGLKGDTEGAGFPGSRGYLGPTGNVGRPGNPGQKGQKGAKGR

Parental  GNLFHLP-NVVRLVNGK-VPHEGR-VEIFHEGIWGTICDDRWEIRVATVICRSLGYKGAKAVHKAAYFGQ
          ...F.LP...VRL.NGK..P..GR...IF.EG...TI.DDRWEI.VA.VI..SL.YKG..AVHK.AYFGQ
Retrocopy RSIFPLP<KTVRLANGK<RPQKGR<KDIFQEGR*STIWDDRWEIQVASVIW*SLEYKGVQAVHKVAYFGQ

Parental  GTGPIWLNE-FCFGRESSIDQCNIRQ
          GTGPIWL.E.FCFGR..S...CNIRQ
Retrocopy GTGPIWLTEVFCFGRKLSMEKCNIRQ

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	0.42 RPM
SRP017611_liver	0.00 RPM	21.85 RPM
SRP040447_lung	0.00 RPM	63.46 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.21 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_454 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_454 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.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000022785	1 retrocopy	retro_cpor_454 ,