RetrogeneDB ID: retro_cpor_745

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_26:18149015..18149543(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSCPOG00000012266
• Aliases: None
• Description: None

Sequence

>retro_cpor_745
CAAAGAAGGAAAGAGAGACAGGTCAAGTCTTTGAAAACATCAAGATACACTTCACTCTCAAGTTCTCCAACAGGCCCTTA
ATCAAAGGTGTTAGATAAACCCACCAGGCTAACTGCAAAGGAACTTGCTGAGGCTGTAAGGAAGTGGGCTGTGGAAAATC
TTGAAAGGTCACAGAATAACTTGCCCAGGATTTTTTTAATTCAAGGTGGGGCCTACAACACCTTTACTCACTGAGCAACC
AGAGAAGCAAGGGACTAAAGCATCAGAAAGTACAGAATTATTTGAAGATAGTAAACTCAGCAGTTACTCAAAAGCAATAG
CATCCAAAACTAAAGAGATTAAGCATGCTTACTGACAACACAGTGAGAATTTAGGATGGTGGTGAAAATGCTGATTAAAG
AAGAGCCTTCCCTGGAAAAGGCCATACACTTTGCACTTAGGCACAATTTACATTAGACAGCAGAGTGATATGTTGAAGAA
ATCAGGCACTTCAATGCAGAATATGATATTTCTCATGATTTTGGAGAG

Alignment

ORF - retro_cpor_745 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.89 %
• Parental protein coverage: 54.77 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ERGKERPVPSMKTSRDTSPSSSPAGPSSKALDKPSRLTEKELAEAASKWAAEKLEKSEETNVP-GISEFQ
          .R.KER.V.S.KTSR.TS.SSSP.GP.SK.LDKP.RLT.KELAEA..KWA.E.LE.S...N.P.G...F.
Retrocopy QRRKERQVKSLKTSRYTSLSSSPTGP*SKVLDKPTRLTAKELAEAVRKWAVENLERS-QNNLP>GFF*FK

Parental  VGPTTQLFIENPEETDTNATDSTELFEDSQLSSRSKAIALKTKEIEQVYRQDCETFG-MVVKMLIEKDPS
          VGPTT.L..E.PE...T.A..STELFEDS.LSS.SKAIA.KTKEI...Y.Q..E..G.MVVKMLI...PS
Retrocopy VGPTTPLLTEQPEKQGTKASESTELFEDSKLSSYSKAIASKTKEIKHAY*QHSENLG<MVVKMLIKEEPS

Parental  LEKSIQFALRQNLHEIGERCVEELKHFIAEYDTSTQDFGE
          LEK.I.FALR.NLH...E..VEE..HF.AEYD.S..DFGE
Retrocopy LEKAIHFALRHNLH*TAE*YVEEIRHFNAEYDIS-HDFGE

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	10.99 RPM
SRP017611_kidney	0.00 RPM	12.77 RPM
SRP017611_liver	0.00 RPM	10.71 RPM
SRP040447_lung	0.00 RPM	13.27 RPM
SRP040447_skeletal_muscle	0.00 RPM	4.06 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_745 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_745 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010693	1 retrocopy	retro_chof_1231,
Callithrix jacchus	ENSCJAG00000017726	1 retrocopy	retro_cjac_1547,
Cavia porcellus	ENSCPOG00000012266	2 retrocopies	retro_cpor_744, retro_cpor_745 ,
Dasypus novemcinctus	ENSDNOG00000002007	1 retrocopy	retro_dnov_1790,
Equus caballus	ENSECAG00000016067	1 retrocopy	retro_ecab_209,
Mus musculus	ENSMUSG00000036167	3 retrocopies	retro_mmus_1657, retro_mmus_3561, retro_mmus_79,
Otolemur garnettii	ENSOGAG00000004012	2 retrocopies	retro_ogar_1387, retro_ogar_2103,
Tarsius syrichta	ENSTSYG00000010740	1 retrocopy	retro_tsyr_2044,