RetrogeneDB ID: retro_cpor_1335

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_7:21922494..21923019(-)
• Located in intron of: ENSCPOG00000007363

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCNP
• Ensembl ID: ENSCPOG00000010610
• Aliases: None
• Description: None

Sequence

>retro_cpor_1335
ATAGCGGACCAAAAGGCGGGAGAGGAGAAGCCTGAGAAGTCCAAGCGAGCTGGAGCCGCTGGAGGACCTGAAGAAGCAGA
AAAACCTGTGAAAACTAAGACTGTTCTTTCAGTAATGGAGGGGAAAGTTCCAGTCACAGCACTGAGAAGTGATCCGCTGA
AGAAGCTGCAGACATCCCAACAAAGTCTACAAAGATCTCCAAATTTGGATTTGCCATAGGTGGTCAGACAGCAAAGAAAG
CATCAGCTATATCCATCAAACTTGGATCAAGTAAGCCTAAAGAAACTGTTCCAACTCTTGCTCCAAAAATCCTTTCAGTA
CAGCAGCTTTTAATGAAGATAAAGATAGTGAACCTGAGGAAATGCCTCCAGAAGCAAAGATAAGGATGAAGAATACTGGA
AGGGATACACTGACATCAGCTGGACCAAACTCTTTCAATAAAGGAAAGCATAGGTTTTCTGATAACCAGAAGCTAGGGAA
TGGAATATAAAATCTCACCTTGGGAACGTCCACGACCAAGACAAT

Alignment

ORF - retro_cpor_1335 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.29 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MADRKAGEEKPEKSKRAGAAGGPEEEAEKPVKTKTVSS-SNGGESSSRSAEKRSAEEEAADLPTKPTKIS
          .AD.KAGEEKPEKSKRAGAAGGPEE.AEKPVKTKTV.S.SNGGESSS.S.EK.SAEE.AAD.PTK.TKIS
Retrocopy IADQKAGEEKPEKSKRAGAAGGPEE-AEKPVKTKTVLS<SNGGESSSHSTEK*SAEE-AADIPTKSTKIS

Parental  KFGFAIGSQTAKKASAISIKLGSSKPKETVPTLAPKTLSV-AAAFNEDEDSEPEEMPPEAKMRMKNIGRD
          KFGFAIG.QTAKKASAISIKLGSSKPKETVPTLAPK.LSV..AAFNED.DSEPEEMPPEAK.RMKN.GRD
Retrocopy KFGFAIGGQTAKKASAISIKLGSSKPKETVPTLAPKILSV<TAAFNEDKDSEPEEMPPEAKIRMKNTGRD

Parental  TPTSAGPNSFNKGKHGFSDNQKLW-ERNIKSHLGNVHDQDN
          T.TSAGPNSFNKGKH.FSDNQKL..E.NIKSHLGNVHDQDN
Retrocopy TLTSAGPNSFNKGKHRFSDNQKLG<EWNIKSHLGNVHDQDN

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	0.06 RPM	27.78 RPM
SRP017611_kidney	0.00 RPM	26.90 RPM
SRP017611_liver	0.00 RPM	24.59 RPM
SRP040447_lung	0.13 RPM	21.03 RPM
SRP040447_skeletal_muscle	0.04 RPM	13.56 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1335 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1335 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 10 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007972	11 retrocopies	retro_chof_1170, retro_chof_1215, retro_chof_2070, retro_chof_2280, retro_chof_2290, retro_chof_2553, retro_chof_2575, retro_chof_594, retro_chof_651, retro_chof_806, retro_chof_819,
Callithrix jacchus	ENSCJAG00000000508	6 retrocopies	retro_cjac_101, retro_cjac_1569, retro_cjac_1722, retro_cjac_3205, retro_cjac_3332, retro_cjac_401,
Cavia porcellus	ENSCPOG00000010610	2 retrocopies	retro_cpor_1335 , retro_cpor_443,
Dasypus novemcinctus	ENSDNOG00000008873	5 retrocopies	retro_dnov_1606, retro_dnov_259, retro_dnov_370, retro_dnov_910, retro_dnov_98,
Gorilla gorilla	ENSGGOG00000025423	4 retrocopies	retro_ggor_882, retro_ggor_901, retro_ggor_902, retro_ggor_994,
Loxodonta africana	ENSLAFG00000005518	2 retrocopies	retro_lafr_1189, retro_lafr_458,
Macaca mulatta	ENSMMUG00000017782	3 retrocopies	retro_mmul_1312, retro_mmul_1377, retro_mmul_2598,
Mustela putorius furo	ENSMPUG00000011696	1 retrocopy	retro_mputfur_850,
Otolemur garnettii	ENSOGAG00000001821	4 retrocopies	retro_ogar_2216, retro_ogar_2465, retro_ogar_3320, retro_ogar_652,
Procavia capensis	ENSPCAG00000007007	3 retrocopies	retro_pcap_161, retro_pcap_194, retro_pcap_273,