RetrogeneDB ID: retro_cpor_663

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_212:770227..770740(-)
• Located in intron of: ENSCPOG00000024855

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPA
• Ensembl ID: ENSCPOG00000010875
• Aliases: None
• Description: None

Sequence

>retro_cpor_663
CAGCCCAAGAGCCAGGAGACACAATTGCCAAGAAGGCTGTGCAGGGTGGGGTGGTAGCCCCTGTGGTGGGACCTGTCCAG
GACCTTGTCCCAGGCATGCCACCAATAACTCAGACCCCCATATCATGTATCACATGCCGGGCCTACCACAAAACGTGTTG
CTTCCTGGTATGATTCTGTCTCCAGGCCTTGAACCAGGGCAGACTCCCCCTATGGCCATGCCCTAAAGCAGCTTATGAAA
AGACAGATGCTTCCTGCCTATCCTCTCTAGGTGAATCCACCAAATCACATCCTGTTCCTCACCAACCTGCCAGAGGAGAC
CAATAAGCTCAATTTGTCTATGCCCTTCAACCACTTTCCTGGCTGAAAGAAGCTCTCCCTGGAACCTGGGTGGCATGGTA
TCGCCTTCGTGAAGTTTGACAATAATTAGATGCTGGCAAGGGCTGCTAGTGATATTCTGCAGGGCTTTAAGATCACCCAG
AACAATGCAATGAAGATCTCCTTTGTCAAGAAG

Alignment

ORF - retro_cpor_663 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.14 %
• Parental protein coverage: 59.38 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KPKSQETPS-AKKAVQGGAAAPVVGAVQGPVPGMPPMTQAP-RIMHHMPGQPPYMPPPGMIPPPGLAPGQ
          .PKSQET...AKKAVQGG..APVVG.VQ..VPGMPP.TQ.P..IM.HMPG.P.....PGMI..PGL.PGQ
Retrocopy QPKSQETQL<AKKAVQGGVVAPVVGPVQDLVPGMPPITQTP<HIMYHMPGLPQNVLLPGMILSPGLEPGQ

Parental  IPPGAMP-PQQLMPGQMPPAQPLSENPPNHILFLTNLPEETNELMLSMLFNQFPGFKEVRLVPGRHDIAF
          .PP.AMP...QLM..QM.PA.PL..NPPNHILFLTNLPEETN.L.LSM.FN.FPG.K...L.PG.H.IAF
Retrocopy TPPMAMP<LKQLMKRQMLPAYPL*VNPPNHILFLTNLPEETNKLNLSMPFNHFPG*KKLSLEPGWHGIAF

Parental  VEFDNE-VQAGAARDALQGFKITQNNAMKISFAKK
          V.FDN....A.AA.D.LQGFKITQNNAMKISF.KK
Retrocopy VKFDNN*MLARAASDILQGFKITQNNAMKISFVKK

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	16.05 RPM
SRP017611_kidney	0.00 RPM	15.60 RPM
SRP017611_liver	0.00 RPM	8.44 RPM
SRP040447_lung	0.00 RPM	22.37 RPM
SRP040447_skeletal_muscle	0.00 RPM	11.63 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_663 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_663 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 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000005091	1 retrocopy	retro_cfam_1114,
Callithrix jacchus	ENSCJAG00000014865	1 retrocopy	retro_cjac_287,
Cavia porcellus	ENSCPOG00000010875	1 retrocopy	retro_cpor_663 ,
Myotis lucifugus	ENSMLUG00000000219	1 retrocopy	retro_mluc_1517,
Monodelphis domestica	ENSMODG00000007912	1 retrocopy	retro_mdom_447,
Mustela putorius furo	ENSMPUG00000017681	1 retrocopy	retro_mputfur_593,
Mus musculus	ENSMUSG00000061479	6 retrocopies	retro_mmus_275, retro_mmus_3374, retro_mmus_469, retro_mmus_888, retro_mmus_889, retro_mmus_958,
Otolemur garnettii	ENSOGAG00000002864	1 retrocopy	retro_ogar_2046,
Pteropus vampyrus	ENSPVAG00000001494	1 retrocopy	retro_pvam_832,