RetrogeneDB ID: retro_cpor_935

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_35:8393163..8394234(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000004962
• Aliases: None
• Description: None

Sequence

>retro_cpor_935
GTCTCCACCGCCGACCAATGGGTGCAGACTGTGTTTGGCACTGACTTCTGAGACCTGGCTGTCAGCCTCATGTCACCAGT
TTGGAAGGATGAAGAGGACAAGGGGCCCAGGCTTCCTCCAGGGCGATCGGCTCTCTGGACTACCAGGAGTTGGTAGTTGA
CATTGAGTCCAGGCTGAGGATGGAAGGTGTGGAACTGACAAAGAGTGGCAAGATGAAGCTTTTCCAGTACCTTTACTAGA
AGATGATAGTATTGAGGCAGATCTACTTGGTATACCTGGACCAGAGAGCCAGCCTGACTCAACAGAAGTTAATGGAAATA
AAGTGACAAAGAAATTAAGGGCTCTGGACATCAACCTGACCCTGGATCCCAGCGATGGCTCTGCGTTGTCAGAGGATTTG
GATGAAAGTAAGGAGATAGACTTAGATGGCTTGGACATACTATCAGAGAACAGTAATAAATGTGAGTGGGAAGGTGATCT
TCCCAAACTCAAAACTACTGACGTCATTAGAAAACGCTCTGTTACTTAGTACACTACAACAGAAGACAAAGATAACAGAT
AACTCTGGCGCATGTTCAGGACAGGTGATCAGGACGACAGGGCTGACAGGAAAGAACTGAACCCTACAAAAAAGTCATCA
GCCATGGAGGATATTATGGGGATGGATTAAAAGCTGTTGTTGTGTTTGCTGTCTGTTTTACGCCTGAGAGTTTTTGGCCT
AATCATAGATACCTGATGGACAATCTCTTTAAGTATGTTATTGATACTGTGGAGCTGTTAGTAGCAGAAAATTACATACT
AGTTTATTTGAATCGTGCAACAACTTGAAGAAAAATGCCCAGTGTGGGATGGCTCAGGAAAGGCTATCAACAAATCCATA
AAAGGTCACAGAAAAACCTGAAATTTCTAATCATTTTACTTCTCTCTTAGTTTATCAGAACACTTCTGGCTGTTACAAGA
TCATTTATTAGCTCAAAATTTAGCCAAAAAGTTAGATACATCTTTAATTTGGTGGAACTAGCAGATCTAGGTCCAGTGGA
GTATGTTGGCATACCAGAATGCATCAAACAA

Alignment

ORF - retro_cpor_935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.13 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  VSTADRGERAPLGADFCDLAVSPTSPTWRGEED-EGAEAFSGALGSLGCQELAADIESRLRMEGVELKE-
          VSTAD.......G.DF.DLAVS..SP.W..EED..GA.A.S.A.GSL..QEL..DIESRLRMEGVEL...
Retrocopy VSTADQWVQTVFGTDF*DLAVSLMSPVWKDEED<QGAQASSRAIGSLDYQELVVDIESRLRMEGVELTK<

Parental  EWQDEDFPIPLPEDDSIEADILGVPGPENQPDSPEVNGNKVRKKLIAPDISLTLDPSDGSVLSDDLDESG
          EWQDE.FP.PL.EDDSIEAD.LG.PGPE.QPDS.EVNGNKV.KKL.A.DI.LTLDPSDGS.LS.DLDES.
Retrocopy EWQDEAFPVPLLEDDSIEADLLGIPGPESQPDSTEVNGNKVTKKLRALDINLTLDPSDGSALSEDLDESK

Parental  EVDLDGLDTPSENSNEFEWEDDLPKPKTTEVIRKGSVTEYTAAEEKEDGRRWRMFRIGEQDHRVDMKAI-
          E.DLDGLD..SENSN..EWE.DLPK.KTT.VIRK.SVT.YT..E.K.....WRMFR.G.QD.R.D.K...
Retrocopy EIDLDGLDILSENSNKCEWEGDLPKLKTTDVIRKRSVT*YTTTEDKDNR*LWRMFRTGDQDDRADRKEL<

Parental  EPYKKVISHGGYYGDGLNAIVVFAVCFMPESGQPNYRYLMDNLFKYVIGTLELLVAENYMIVYLNGATTR
          EPYKKVISHGGYYGDGL.A.VVFAVCF.PES..PN.RYLMDNLFKYVI.T.ELLVAENY..VYLN.ATT.
Retrocopy EPYKKVISHGGYYGDGLKAVVVFAVCFTPESFWPNHRYLMDNLFKYVIDTVELLVAENYILVYLNRATT*

Parental  RKMPSLGWLRKCYQQIDRRLRKNLKSLIIVHPSWFIRTLLAVTRPFISSKFSQKIRYVFNLAELAELVPM
          RKMPS.GWLRK.YQQI..R..KNLK.LII...S.FIRTLLAVTR.FISSKFSQK.RY.FNL.ELA.L.P.
Retrocopy RKMPSVGWLRKGYQQIHKRSQKNLKFLIILLLS*FIRTLLAVTRSFISSKFSQKVRYIFNLVELADLGPV

Parental  EYVGIPECIKQ
          EYVGIPECIKQ
Retrocopy EYVGIPECIKQ

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	8.28 RPM
SRP017611_kidney	0.00 RPM	9.00 RPM
SRP017611_liver	0.04 RPM	7.62 RPM
SRP040447_lung	0.00 RPM	28.47 RPM
SRP040447_skeletal_muscle	0.00 RPM	12.47 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_935 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_935 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014722	1 retrocopy	retro_cjac_2997,
Cavia porcellus	ENSCPOG00000004962	2 retrocopies	retro_cpor_393, retro_cpor_935 ,
Mus musculus	ENSMUSG00000011958	1 retrocopy	retro_mmus_3251,