RetrogeneDB ID: retro_cpor_686

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_23:32175144..32175668(+)
• Located in intron of: ENSCPOG00000005366

Retrocopy information

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

Parental gene information

• Parental gene symbol: SYCP3
• Ensembl ID: ENSCPOG00000001202
• Aliases: None
• Description: None

Sequence

>retro_cpor_686
GCAGCACCTGCAAGAAAGGTTCCAGGAATTGGTAAGTGGGAAAAAAGGTCTTCTGCAGAAATACTTGAAGATATGGGGGG
TGAAGTACAGATTATGCTGGAAAAATTTGGAGCTGACATTAACAAGGCTCTTCTTGGCAAGGCTCTTGCCAAGAGAAAAA
CACTAGAAGTGTATACCAAGGCTTCTTTCAAATCCAGTAGCCAGAAAATTGAACATGTGTGGGAAACATAACAAGAACAA
AGGCCGACACTTAACCAAGAGTATTCTGAGCAGTTCCTGACCATGTTTCAGCAGTGGCATACAGATTTGAAGAAAGCGGA
GGAACAAGAAGAGAAACTGGTGAGTATAATGTGACAATAACAAAAGGCTTTTCAACAGTCTAGAATTGTTCAAACTTAGA
GACTGAAAACAGACAGTTATATATGGAGTTCATAGAAGAGTCTGGAGGACTGGAGAAGAATCATGATAATCTTCTTAGAG
GGACTCAAACAGATATAAACTTAAAAAAAGAAATGGCTATGTTG

Alignment

ORF - retro_cpor_686 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.6 %
• Parental protein coverage: 74.35 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AEAEEKVPAMDKRGKKRSSAELLEDMGGEVQNMLEKFGADINKAL----LVKRKRLEMYTKASFKSSSQK
          A....KVP...K...KRSSAE.LEDMGGEVQ.MLEKFGADINKAL....L.KRK.LE.YTKASFKSSSQK
Retrocopy AAPARKVPGIGK-WEKRSSAEILEDMGGEVQIMLEKFGADINKALLGKALAKRKTLEVYTKASFKSSSQK

Parental  IEHVWKTQQEQRQKLNQEYSEQFLAVFQQWDTDLKKAEEQEEKLVSIMRQQQKVFQQSRIVQNQRLKTVR
          IEHVW.T.QEQR..LNQEYSEQFL..FQQW.TDLKKAEEQEEKLVSIM.Q.QK.FQQSRIVQ..RLKT..
Retrocopy IEHVWET*QEQRPTLNQEYSEQFLTMFQQWHTDLKKAEEQEEKLVSIM*Q*QKAFQQSRIVQT*RLKTDS

Parental  QLYEQYIKSLED-LEKNHDSLLSGTQNE--LKKEMAML
          .......KSLED.LEKNHD.LL.GTQ....LKKEMAML
Retrocopy YIWSS-*KSLED<LEKNHDNLLRGTQTDINLKKEMAML

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	0.98 RPM
SRP017611_kidney	0.00 RPM	1.99 RPM
SRP017611_liver	0.00 RPM	2.39 RPM
SRP040447_lung	0.00 RPM	1.34 RPM
SRP040447_skeletal_muscle	0.00 RPM	0.69 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_686 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_686 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.

---

Parental genes homology:

Parental genes homology involve 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013389	2 retrocopies	retro_chof_1384, retro_chof_2693,
Callithrix jacchus	ENSCJAG00000001658	1 retrocopy	retro_cjac_2710,
Cavia porcellus	ENSCPOG00000001202	1 retrocopy	retro_cpor_686 ,
Dasypus novemcinctus	ENSDNOG00000017387	2 retrocopies	retro_dnov_2623, retro_dnov_739,
Dasypus novemcinctus	ENSDNOG00000017624	3 retrocopies	retro_dnov_2294, retro_dnov_2402, retro_dnov_420,
Echinops telfairi	ENSETEG00000007664	1 retrocopy	retro_etel_1510,
Myotis lucifugus	ENSMLUG00000010711	2 retrocopies	retro_mluc_1098, retro_mluc_1839,
Mus musculus	ENSMUSG00000067764	1 retrocopy	retro_mmus_1085,
Mus musculus	ENSMUSG00000072479	1 retrocopy	retro_mmus_1782,
Otolemur garnettii	ENSOGAG00000024543	1 retrocopy	retro_ogar_633,
Rattus norvegicus	ENSRNOG00000017224	1 retrocopy	retro_rnor_1728,
Ictidomys tridecemlineatus	ENSSTOG00000001853	1 retrocopy	retro_itri_931,