RetrogeneDB ID: retro_cpor_16

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_31:4061022..4061979(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000008036
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: PRPS2
• Ensembl ID: ENSCPOG00000007206
• Aliases: None
• Description: Ribose-phosphate pyrophosphokinase [Source:UniProtKB/TrEMBL;Acc:H0V9K0]

Sequence

>retro_cpor_16
ATGCCGAACATCAAAATCTTCAGCGGCAGCTCGCACCAGGATTTATCCCAGAAAATTGCCGACCGCCTCGGCCTGGAGCT
GGGTAAGGTGGTGACTAAGAAATTCAGTAACCAGGAAACGTGTGTGGAAATCGGCGAGAGTGTGCGTGGGGAAGACGTCT
ACATCGTTCAGAGTGGGTGTGGCGAAATCAACGACGGGCTCATGGAGCTTTTGATCATGATCAATGCCTGCAAGATTGCT
TCAGCCAGCCGCGTTACCGCGGTCATCCCGTGCTTCCCCTACGCGCGGCAGGATAAGAAGGATAAGAGCCGGGCCCCGAT
CTCGGCGAAGCTCGTGGCAAATATGCTGTCGATCGCGGGCGCGGATCATATCATCACCATGGACCTGCATGCTTCCCAAA
TCCAGGGCTTTTTTGATATCCCAGTAGACAATCTGTATGCCGAACCGGCTGTCCTGAAGTGGATAAAGGAGAATATTCCC
GATTGGAAAAACTGCATTGTTGTCTCCCCCGACGCCGGCGGAGCCAAAAGAGTCACTTCGATTGCAGACCGCCTGAATGT
GGAGTTTGCCTTGATTCATAAAGAGCGGAAGAAAGCCAATGAAGTGGACCGCATGGTGCTGGTGGGAGACGTGAAGGATC
GTGTGGCCATCCTTGTGGATGACATGGCTGATACCTGTGGAACAATCTGCCACGCAGCCGACAAACTTGCCTCAGCTGGG
GCCACCAGAATCTATGCGATCTTGACCCACGGAATCTTTTCTGGCCCAGCCATTGCTCGCATCGACAGTGCATGCTTTGA
AGCAGTAGTGGTCACCAATACCATACCTCAGGAAGATAAGATGAAGCACTGCTCCAAAATACAGGTGATTGACATCTCCA
TGATTCTTGCAGAAGCCATCCGGAGGACTCACAATGGGGAATCTGTTTCCTACCTGTTCAGCCATGTTCCTTTGTAG

Alignment

ORF - retro_cpor_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.82 %
• Parental protein coverage: 96.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPNIVLFSGSSHQDLSQRVADRLGLELGKVVTKKFSNQETSVEIGESVRGEDVYIIQSGCGEINDNLMEL
          MPNI..FSGSSHQDLSQ..ADRLGLELGKVVTKKFSNQET.VEIGESVRGEDVYI.QSGCGEIND.LMEL
Retrocopy MPNIKIFSGSSHQDLSQKIADRLGLELGKVVTKKFSNQETCVEIGESVRGEDVYIVQSGCGEINDGLMEL

Parental  LIMINACKIASSSRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSVAGADHIITMDLHASQIQGFFDI
          LIMINACKIAS.SRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLS.AGADHIITMDLHASQIQGFFDI
Retrocopy LIMINACKIASASRVTAVIPCFPYARQDKKDKSRAPISAKLVANMLSIAGADHIITMDLHASQIQGFFDI

Parental  PVDNLYAEPAVLQWIRENISEWRNCIIVSPDAGGAKRVTSIADRLNVEFALIHKERKKANEVDRMVLVGD
          PVDNLYAEPAVL.WI.ENI..W.NCI.VSPDAGGAKRVTSIADRLNVEFALIHKERKKANEVDRMVLVGD
Retrocopy PVDNLYAEPAVLKWIKENIPDWKNCIVVSPDAGGAKRVTSIADRLNVEFALIHKERKKANEVDRMVLVGD

Parental  VKGRVAILVDDMADTCGTICFAADRLLSAGATKVYAILTHGIFSGPAISRINNASFEAVVVTNTIPQEDK
          VK.RVAILVDDMADTCGTIC.AAD.L.SAGAT..YAILTHGIFSGPAI.RI..A.FEAVVVTNTIPQEDK
Retrocopy VKDRVAILVDDMADTCGTICHAADKLASAGATRIYAILTHGIFSGPAIARIDSACFEAVVVTNTIPQEDK

Parental  MKHCPKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
          MKHC.KIQVIDISMILAEAIRRTHNGESVSYLFSHVPL
Retrocopy MKHCSKIQVIDISMILAEAIRRTHNGESVSYLFSHVPL

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	3.51 RPM	7.76 RPM
SRP017611_kidney	6.07 RPM	24.50 RPM
SRP017611_liver	4.31 RPM	5.40 RPM
SRP040447_lung	10.77 RPM	28.47 RPM
SRP040447_skeletal_muscle	2.92 RPM	4.13 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_16 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_16 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007206	1 retrocopy	retro_cpor_16 ,
Dipodomys ordii	ENSDORG00000007577	2 retrocopies	retro_dord_223, retro_dord_605,
Felis catus	ENSFCAG00000026323	1 retrocopy	retro_fcat_527,
Monodelphis domestica	ENSMODG00000017334	4 retrocopies	retro_mdom_1323, retro_mdom_1359, retro_mdom_258, retro_mdom_834,
Sorex araneus	ENSSARG00000007710	1 retrocopy	retro_sara_18,