RetrogeneDB ID: retro_cpor_1032

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_4:19685711..19686377(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPC25
• Ensembl ID: ENSCPOG00000005926
• Aliases: None
• Description: None

Sequence

>retro_cpor_1032
ATGGTAGAGGATGAATGGGAACTGTTCGATAAAAGCATAAATGAATTTGGAAATAAGTTCTGAAACACTCTCAATGACAC
CTCCATCAGATGGTGGGACTAAGAGATGCCTGTAAGGACTCCATAAACGGTCTGGCAGAAAAGTTCTCTGTCAAATTAAA
GGAAGAGAATGAATGGTTGAGATGTTTCTGGAATATCAAGAACAGGTCTGCAAGCATAATAAGCTGATTCAAGAAAAAGA
AGATAATCTTTTAAAGCTGCTTGCTGAAAAATGAAAGGCTAAAAGTAGGAACTGGAAGTCCTAACCACAAATATTCAGGA
TCTTGAAGAATATTCTAGGAAGAAAGAAACTATTTCCACTGCTAACAGAGCTAATGAAAGATTGAAAAGGCTTCAGAGGT
CAGCAGACTTGTATAAAGATTGACTTGGACTAGAAATTAGAAACTGTATGGGGATAAACTGCAGATTTTATTCACTAGTA
TTGACTCTAAGCATCCTGAAAACCCATTTATGTTTTCCTTGTATCTAAATGAAACAGGGGACTATAAAGTGTCAGATAGT
GCTCCTTGAGTGCCTAGCAGAATTTCAAGAGAATGTAAGGAAGACCAACAATTTTTCAGTTTTTCTTGCCAATGTTGGGA
AAGCTTTTACTGCTATGGTTTATAAT

Alignment

ORF - retro_cpor_1032 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.81 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MVEDELALFDKSINEFGNKFRNTLSDTPC-QMLGLRDACKDSIKTLAEKLSVKLKEEEK-MVEMFLEYQN
          MVEDE..LFDKSINEFGNKF.NTL.DT...QM.GLRDACKDSI..LAEK.SVKLKEE...MVEMFLEYQ.
Retrocopy MVEDEWELFDKSINEFGNKF*NTLNDTSI<QMVGLRDACKDSINGLAEKFSVKLKEENE<MVEMFLEYQE

Parental  QVCKQNKLI-QEKKDNLLKLIAEVKGKTQ-EMEVLTANIQDLKEEYSRKRETISTANKANEERLKRLQKS
          QVCK.NKLI.......L..L....K.K...E.EVLT.NIQDL.EEYSRK.ETISTAN.ANE.RLKRLQ.S
Retrocopy QVCKHNKLIQEKEDNLLKLLAEK*KAKSR<ELEVLTTNIQDL-EEYSRKKETISTANRANE-RLKRLQRS

Parental  ADLYKDRLGLEIR-KIYGDKLQFIFTNIDSKHPENPFMFSLRLNEAGDYEVSDSAPHLECLAEFQENVRK
          ADLYKD.LGLEIR.K.YGDKLQ..FT.IDSKHPENPFMFSL.LNE.GDY.VSDSAP..............
Retrocopy ADLYKD*LGLEIR<KLYGDKLQILFTSIDSKHPENPFMFSLYLNETGDYKVSDSAP*VP--SRISRECKE

Parental  TNNFSAFLANVRKAF-TATVYN
          ...F..F.......F.TA.VYN
Retrocopy DQQFFSFSCQCWESF>TAMVYN

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	0.12 RPM
SRP017611_kidney	0.00 RPM	0.63 RPM
SRP017611_liver	0.00 RPM	1.04 RPM
SRP040447_lung	0.03 RPM	3.46 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.29 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1032 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1032 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013303	4 retrocopies	retro_chof_1070, retro_chof_1541, retro_chof_2326, retro_chof_744,
Cavia porcellus	ENSCPOG00000005926	1 retrocopy	retro_cpor_1032 ,
Dasypus novemcinctus	ENSDNOG00000004429	1 retrocopy	retro_dnov_826,
Echinops telfairi	ENSETEG00000015642	1 retrocopy	retro_etel_1554,
Loxodonta africana	ENSLAFG00000004668	1 retrocopy	retro_lafr_497,
Monodelphis domestica	ENSMODG00000007753	1 retrocopy	retro_mdom_1828,
Tupaia belangeri	ENSTBEG00000012559	1 retrocopy	retro_tbel_2798,
Tursiops truncatus	ENSTTRG00000006112	1 retrocopy	retro_ttru_574,