RetrogeneDB ID: retro_cpor_457

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_16:37491550..37492204(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CDK4
• Ensembl ID: ENSCPOG00000002670
• Aliases: None
• Description: None

Sequence

>retro_cpor_457
GAGATCAAGGTGACCCCAGTGTCTGAGTATGTAGACCAAGACCTAAAGATGGATCTGGACAAGACACCTCCGCTAGGCTT
GCAAACTGAAACCATTAAGGATCTGATGCTCCAGTTTCTAAAAGGCCTAGATTTTCTGCACGCTCTCTGCATTGTTTACC
AACACCTAAAACCAGAGGACATTCTGGTGATTAATGGTGGGATAGTCAAGCTGGCAGACTTTGGCCTCGCCAGAATCTAA
AGCTTCCTGATGGCCCTTACACCACTGGTGGTTACACTCTGATACCAGGCTCCTGAAATTCTTCTGAAATCTATATATGT
AACCCCTGTGGACATGTGGTGTGTGGCCTGTATCTTTGCAGAGATGTTTCATCAAAAGTCTCTTTTCTGTGGAAACTCTG
AAGCTGATCAATTGGGCAGAATCTTTGACCTGATTGGGCTGCCTCCGGAGCATGACTGACGGAGAGCTGTATCTTTATCC
CTAGGAGCCTTTACCTCTGGAGGGCCTCTCATAGGAGGGTCAGTGGGATCTGAGATGGAGGAGTCTGGAGCAGAGCTGCT
GCCAAAAATGCTGACATTTAATCTTCACAAGCAAGCCTCTGCCTTCTGAGCCCTGCAACACCCTTACCTACGTAAGAAAG
ATGGGGACCCAGAG

Alignment

ORF - retro_cpor_457 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.56 %
• Parental protein coverage: 71.95 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EIKVTLVFEHVDQDLRTYLDKAPPPGLPVETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVK
          EIKVT.V.E.VDQDL...LDK.PP.GL..ETIKDLM.QFL.GLDFLHA.CIV...LKPE.ILV..GG.VK
Retrocopy EIKVTPVSEYVDQDLKMDLDKTPPLGLQTETIKDLMLQFLKGLDFLHALCIVYQHLKPEDILVINGGIVK

Parental  LADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGK
          LADFGLARI.S..MALTP.VVTL.Y.APE.LL.S.Y.TPVDMW.V.CIFAEMF..K.LFCGNSEADQLG.
Retrocopy LADFGLARI*SFLMALTPLVVTL*YQAPEILLKSIYVTPVDMWCVACIFAEMFHQKSLFCGNSEADQLGR

Parental  IFDLIGLPPEDDWPRDVSLPRGAFSPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRALQHSYL
          IFDLIGLPPE.D..R.VSL..GAF...GP....SV..EMEESGA.LL..MLTFN.HK..SAF.ALQH.YL
Retrocopy IFDLIGLPPEHD*RRAVSLSLGAFTSGGPLIGGSVGSEMEESGAELLPKMLTFNLHKQASAF*ALQHPYL

Parental  HKEEGDPE
          .K..GDPE
Retrocopy RKKDGDPE

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	14.03 RPM
SRP017611_kidney	0.00 RPM	36.85 RPM
SRP017611_liver	0.00 RPM	23.46 RPM
SRP040447_lung	0.00 RPM	44.39 RPM
SRP040447_skeletal_muscle	0.03 RPM	16.45 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_457 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_457 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 7 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000007160	1 retrocopy	retro_btau_738,
Callithrix jacchus	ENSCJAG00000006697	3 retrocopies	retro_cjac_2163, retro_cjac_2891, retro_cjac_2951,
Cavia porcellus	ENSCPOG00000002670	1 retrocopy	retro_cpor_457 ,
Cavia porcellus	ENSCPOG00000005402	3 retrocopies	retro_cpor_1414, retro_cpor_1422, retro_cpor_200,
Dasypus novemcinctus	ENSDNOG00000014245	1 retrocopy	retro_dnov_145,
Macropus eugenii	ENSMEUG00000014609	1 retrocopy	retro_meug_23,
Myotis lucifugus	ENSMLUG00000023651	2 retrocopies	retro_mluc_1137, retro_mluc_354,