RetrogeneDB ID: retro_cpor_481

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_166:1332114..1333248(+)
• Located in intron of: ENSCPOG00000021195

Retrocopy information

• Ensembl ID: ENSCPOG00000023934
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUP43
• Ensembl ID: ENSCPOG00000010815
• Aliases: None
• Description: None

Sequence

>retro_cpor_481
ATGGAGAGTATTTGTGCGAAGTTTGTGTCTCAGAAAATAAGCAAAACCCGCTGGCGACCGTTGCCTGCCGGGAGCCTGCA
GACCACAGAGACTTTTGCTACGGGATCTTGGGACAATGAGGACAATTATGTTTCACTGTGGTCTATTGGAGATTTTGGAA
ATCTGGACTCTGATGGAGGGTTTGAAGGAGACCATCAATTATTATGCGAAATCAGACATGGTGGTGATGTCATGGATTTA
CAGTTTTTTGACCAGGAAAGAACTGTGGCTGCTTCATCAACCGGATGTGTAAGAGTTTTCCTTCACCATACAAACCATCA
GACCTTATCAATCCACCAGCAGCGGAACAGCCCATCACCACACAGAGTCTTACAGTGCCCATAGAGGTGCACCATGCACA
GGTATTGTGTGTGACAACCCAGAAATTGTCACAGTTGGAGAAGATGGTCGAATAAATCTCTTCAGAATTGATCACAAGGA
AGCTGTAAGAACTATAGACAATGCAGATAGTAGTACACTCCATGCTGTAACTTTCCTTCGAACTCCTGAGATTGTTACAG
TAAATTCAATTGGACAATTAAAAATATGGGATTTCAGACAACAAGGAAATGAGCCTGCTCAAATATTATCAATGAATGGT
GACCGAGTGCCGCTCCACTGTGTGGACAGACATCCCAACCAGCAGCATGTTGTAGCGACAGGTGGCCAGGATGGCATGTT
GAGTATTTGGGATGTCAGACAAGGCACAATGCCTGTATCTCTGCTAAAGGCTCATGAAGCTGAAATGTGGGAAGTTCACT
TTCATCCATCCAAACCAGATCATCTATTCACTTGTTCTGAAGATGGATCCCTCTGGCACTGGGATGCCTCCATAGACATG
CCGGAGAAATCCTCACTCTTTCACCAAGAGGACGATCCAGTACATTTCTGTCTCAGAGCATTAGTAATCAGGCTAATGTT
CACCAGTCTATGATAAGTTCCTGGCTCAGCACTGATCCTGCAAAAGACCGAATTGAGATCACAAGCTTGCTTCCTACCAG
GACTCTGTCTGTGAACAGTTTGGATGTTTTAGGTCCTTGTCTTGTTTGTGGAACTGATGCAGAAGCCATTTATGTTACCA
GACAACTATTTTCA

Alignment

ORF - retro_cpor_481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.44 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MESICAKFVSQKISKTRWRPLPAGSLQTAETFATGSWDNEDNYVSLWSIGDFGNLDSDGGFEGDHQLLCE
          MESICAKFVSQKISKTRWRPLPAGSLQT.ETFATGSWDNEDNYVSLWSIGDFGNLDSDGGFEGDHQLLCE
Retrocopy MESICAKFVSQKISKTRWRPLPAGSLQTTETFATGSWDNEDNYVSLWSIGDFGNLDSDGGFEGDHQLLCE

Parental  IRHGGDVMDLQFFDQERIVAASSTGCITVFLHHTNNQTLSINQQWK-TAHHHTKSYSAYRGAPCTGIVCD
          IRHGGDVMDLQFFDQER.VAASSTGC..VFL.H..N.......Q...TAHHHT.SYSA.RGAPCTGIVCD
Retrocopy IRHGGDVMDLQFFDQERTVAASSTGCVRVFL-HHTNHQTLSIHQQR>TAHHHTESYSAHRGAPCTGIVCD

Parental  NPEIVTVGEDGRINLFRVDHKEAVRTIDNADSSTLHAVTFLRTPEIVTVNSIGQLKIWDFRQQGNEPAQI
          NPEIVTVGEDGRINLFR.DHKEAVRTIDNADSSTLHAVTFLRTPEIVTVNSIGQLKIWDFRQQGNEPAQI
Retrocopy NPEIVTVGEDGRINLFRIDHKEAVRTIDNADSSTLHAVTFLRTPEIVTVNSIGQLKIWDFRQQGNEPAQI

Parental  LSLNGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQGTMPVSLLKAHEAEMWEVHFHPSKPDHLFTC
          LS.NGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQGTMPVSLLKAHEAEMWEVHFHPSKPDHLFTC
Retrocopy LSMNGDRVPLHCVDRHPNQQHVVATGGQDGMLSIWDVRQGTMPVSLLKAHEAEMWEVHFHPSKPDHLFTC

Parental  SEDGSLWHWDASIDMPEKSSLFHQ-GGRSSTFLSQSISNQANVQQS-ISSWLSTDPAKDRIEITSLLPTR
          SEDGSLWHWDASIDMPEKSSLFHQ..GRSSTFLSQSISNQANV.QS.ISSWLSTDPAKDRIEITSLLPTR
Retrocopy SEDGSLWHWDASIDMPEKSSLFHQ<RGRSSTFLSQSISNQANVHQSMISSWLSTDPAKDRIEITSLLPTR

Parental  TLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS
          TLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS
Retrocopy TLSVNSLDVLGPCLVCGTDAEAIYVTRQLFS

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	4.49 RPM
SRP017611_kidney	0.10 RPM	7.43 RPM
SRP017611_liver	0.04 RPM	8.27 RPM
SRP040447_lung	0.00 RPM	11.70 RPM
SRP040447_skeletal_muscle	0.00 RPM	7.08 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_481 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_481 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000009426	1 retrocopy	retro_chof_1765,
Cavia porcellus	ENSCPOG00000010815	1 retrocopy	retro_cpor_481 ,
Macaca mulatta	ENSMMUG00000009830	1 retrocopy	retro_mmul_1962,
Monodelphis domestica	ENSMODG00000016808	2 retrocopies	retro_mdom_199, retro_mdom_353,
Ictidomys tridecemlineatus	ENSSTOG00000013449	1 retrocopy	retro_itri_990,
Tarsius syrichta	ENSTSYG00000000944	1 retrocopy	retro_tsyr_267,