RetrogeneDB ID: retro_cpor_1536

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_95:4051311..4051755(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C19ORF40
• Ensembl ID: ENSCPOG00000011965
• Aliases: None
• Description: None

Sequence

>retro_cpor_1536
AAACTCATTTTTGAGGATGGCCTGATAGTGGTAGATTTTCACCTGTCCAGCACATCTTGCGTTCTCTATATCACTGAAGC
TGATTTAGTGGCAGGAAATGGTTACAGAAATAGACTTGTTTGGGTTAAAAATTCAAGTAATCTTCAAGGGATTGTAGTAG
TTGAAAAGACACAGATGAGTGAACAGTACTTCCCAACCACACCAAAGTTTACCACGCTGGACCTTGGGATAGTGTTGCTT
CCAGTGGCCAACCAGACAGAAGCACCCTGCCTCATCATCCAGTTAGTTCAACAGCAAACCTAAGAGCCCAGTAAGAATCC
TTTCGTTAGGAAGAAAAGGGCTGTGCTCTTTGAGCCATTTCTTCTCTGCACTGTGCAGGAGATCCCAGGAGTGGGGAAAG
TTAAAGCATCTCTTCTGCTCCCGAAGTTTCCATGTATCCAGCAA

Alignment

ORF - retro_cpor_1536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.78 %
• Parental protein coverage: 68.84 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLVFEDGLTVVDFYLSSRSCILYITEADLVAGNGYRKRLVRVRNSSNLQGIVVVEKTQMSEQYFPAIQKF
          KL.FEDGL.VVDF.LSS.SC.LYITEADLVAGNGYR.RLV.V.NSSNLQGIVVVEKTQMSEQYFP...KF
Retrocopy KLIFEDGLIVVDFHLSSTSCVLYITEADLVAGNGYRNRLVWVKNSSNLQGIVVVEKTQMSEQYFPTTPKF

Parental  TVLDLGMVLLPVANQTEASCLIIQLVQEQTKEPRKNPFLRKKRAVLSEPFLLRTVQQIPGVGKVKAPLLL
          T.LDLG.VLLPVANQTEA.CLIIQLVQ.QT.EP.KNPF.RKKRAVL.EPFLL.TVQ.IPGVGKVKA.LLL
Retrocopy TTLDLGIVLLPVANQTEAPCLIIQLVQQQT*EPSKNPFVRKKRAVLFEPFLLCTVQEIPGVGKVKASLLL

Parental  QKFPSIQQ
          .KFP.IQQ
Retrocopy PKFPCIQQ

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	2.30 RPM
SRP017611_kidney	0.10 RPM	4.92 RPM
SRP017611_liver	0.09 RPM	2.09 RPM
SRP040447_lung	0.03 RPM	3.53 RPM
SRP040447_skeletal_muscle	0.00 RPM	1.89 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1536 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1536 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 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000728	2 retrocopies	retro_cjac_1011, retro_cjac_3952,
Cavia porcellus	ENSCPOG00000011965	1 retrocopy	retro_cpor_1536 ,
Dasypus novemcinctus	ENSDNOG00000014134	4 retrocopies	retro_dnov_1817, retro_dnov_2382, retro_dnov_426, retro_dnov_942,
Echinops telfairi	ENSETEG00000002716	1 retrocopy	retro_etel_458,
Loxodonta africana	ENSLAFG00000006401	4 retrocopies	retro_lafr_165, retro_lafr_365, retro_lafr_415, retro_lafr_789,
Myotis lucifugus	ENSMLUG00000013287	1 retrocopy	retro_mluc_522,
Macaca mulatta	ENSMMUG00000017939	1 retrocopy	retro_mmul_788,
Procavia capensis	ENSPCAG00000009727	1 retrocopy	retro_pcap_444,
Sarcophilus harrisii	ENSSHAG00000016372	1 retrocopy	retro_shar_299,