RetrogeneDB ID: retro_cpor_1278

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_64:1780320..1780981(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CCNE2
• Ensembl ID: ENSCPOG00000013401
• Aliases: None
• Description: None

Sequence

>retro_cpor_1278
AGCACCTGTTTACAAGCTAAGCAGCATGCACAACCCAGTCAGACAGACTCCCCCCAAGAAGCCCAGATCATCCAAGCCAA
GAAGAGAAAACAGCACAGGATGTCTAAAAAAGAAGAGCGGAGAAGGTCACCAGGAAACATCAATATGAGATAAGGACTTG
TTGGCCACCTGTATTATCTGGAGGAGTCAGTCCTTGCATTCTCATTAAAGACCCCACAAAGTGATAGGAACAAGTGACTT
TTCTAGATTTACAAACTACAGATTTAAAAATCTTTTTCTTAATCCTTCACCTTTGCCAGATTTAAGCTGGGGATGTTCCC
AGGAGGTTTGTCTAAACATGCTCAAAAAGGAAAACATAATATGTTCATGACAAGAATTTCGAAGTTCTGTGCTGTGACCT
AGAACCACAGATGAGATAATACTTCTAGACTGGCTTTTAGAGGTATGTGAAGTACACACACTTCATAGGGAAACATTTTA
TCTTGCACACGACTTTTTTGATAGATTTATGTTGACACAAAGGAATATAAATAAAAACATGCTTCAGCTCATTGGAATTA
CCTCATTATTCATTGCTTCCAAACTAGAGGAAATCCATGCTCCCAAACTCCCAGAGTTTGCTTATGTCACTGATGGTGCT
TGCAGTGAGGAGGACATTGTA

Alignment

ORF - retro_cpor_1278 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.44 %
• Parental protein coverage: 55.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  STRLQAKQHAQPSQPDSPQEAQIIQAKKRK-AAQDVKKRREEKVTRKHQYEIRNCWPPVLSGGISPCILI
          ST.LQAKQHAQPSQ.DSPQEAQIIQAKKRK..AQDV.KRR.EKVTRKHQYEIR.CWPPVLSGG.SPCILI
Retrocopy STCLQAKQHAQPSQTDSPQEAQIIQAKKRK<TAQDV*KRRAEKVTRKHQYEIRTCWPPVLSGGVSPCILI

Parental  ETP-HKEIGTSDFSRFTSYRFKNLFINPSPLPDLSWGCSQEVWLNMLKKEST-YVHDKNFEGLHCDLEPQ
          ..P.HK.IGTSDFSRFT.YRFKNLF.NPSPLPDLSWGCSQEV.LNMLKKE...YVHDKNFE.L.CDLEPQ
Retrocopy KDP<HKVIGTSDFSRFTNYRFKNLFLNPSPLPDLSWGCSQEVCLNMLKKENI>YVHDKNFEVLCCDLEPQ

Parental  MR-SILLDWLLEVCEVYTLHRETFYLAQDFFDRFMLTQRNINKNMLQLIGITSLFIASKLEEIYAPKLQE
          MR..ILLDWLLEVCEV.TLHRETFYLA.DFFDRFMLTQRNINKNMLQLIGITSLFIASKLEEI.APKL.E
Retrocopy MR<IILLDWLLEVCEVHTLHRETFYLAHDFFDRFMLTQRNINKNMLQLIGITSLFIASKLEEIHAPKLPE

Parental  FAYVTDGACSEEDIV
          FAYVTDGACSEEDIV
Retrocopy FAYVTDGACSEEDIV

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	0.86 RPM
SRP017611_kidney	0.00 RPM	1.47 RPM
SRP017611_liver	0.00 RPM	1.31 RPM
SRP040447_lung	0.00 RPM	4.31 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.87 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1278 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1278 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000013401	1 retrocopy	retro_cpor_1278 ,
Cavia porcellus	ENSCPOG00000014629	1 retrocopy	retro_cpor_13,
Monodelphis domestica	ENSMODG00000007025	2 retrocopies	retro_mdom_392, retro_mdom_707,
Otolemur garnettii	ENSOGAG00000034667	1 retrocopy	retro_ogar_1793,