RetrogeneDB ID: retro_cpor_1052

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_41:12105290..12105830(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMG1
• Ensembl ID: ENSCPOG00000027117
• Aliases: None
• Description: None

Sequence

>retro_cpor_1052
AATGAGTGGTGTAGAAAAACGGACGCTCTACACATCCTCCCAGAGGCTCACCACGTGTATTATCATCTCAAGTCAAACCC
TGCGACTGTCCTCTGTCAGTGAAATTGTTATGTTACTGAAAATCAGCAGTATCAATGGCTAGAAAACGTTTTCAGCTCCT
GGTCCAAAGAACATGCAGGTATCTGTTCTCACATGTTAACATGTCACCAACTATAAAACCTCCAAATCTACTGGCAGCTT
GTCTTCTCTTTTTCTGAAAGCCTTGAAAACACAGAACTTCAAAGATCCTGCATGTTGCTCTTGTTAGAACATCTGAATAT
CATATACAACCTTCCTGCATGAGTGCTGAGTTACTGTCAGGTGTGGCAGTTCCCAGCAATCCTGTGCTACACCAACATGA
TGATGCTAGACCTCCTGATGGCAAAGGCGTTTAGGCCCATACTTTCTTCCAGAAGCCTGAAAGGGCTGGCTAAGAACATT
CCCCAGAGCACAGAGATTCTGAAGAAACTGATAACAAATTCAACTCAGAGTAACATACAT

Alignment

ORF - retro_cpor_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.85 %
• Parental protein coverage: 64.01 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NEWCRTTDTLHMSPSEAHCVFYHLKSTPSVILCQCSCYVAEDQQYQWLDKVFGSCPRKNMQVT--VLTCR
          NEWCR.TD.LH..P.EAH.V.YHLKS.P...LCQ..CYV.E.QQYQWL..VF.S............LTC.
Retrocopy NEWCRKTDALHILP-EAHHVYYHLKSNPATVLCQ*NCYVTENQQYQWLENVFSSWSKEHAGICSHMLTCH

Parental  HV-TDYKTSESTGSLPSPFLKALKTQNFRDPVCCS-LLEQPNIVHDLPAAVLSHCQVWRLPAVLYLCYTD
          ......K...S..SL...FLKALKTQNF.DP.CCS.LLE..NI...LPA.VLS.CQVW..PA...LCYT.
Retrocopy QL>KTSKSTGSLSSL---FLKALKTQNFKDPACCS<LLEHLNIIYNLPA*VLSYCQVWQFPAI--LCYTN

Parental  VMKLDLLTAAAFQPVLASRSLKGLAKNIPQSTEILKRLMTLNEVQSNIY
          .M.LDLL.A.AF.P.L.SRSLKGLAKNIPQSTEILK.L.T.N..QSNI.
Retrocopy MMMLDLLMAKAFRPILSSRSLKGLAKNIPQSTEILKKLIT-NSTQSNIH

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	0.35 RPM	15.47 RPM
SRP017611_kidney	0.42 RPM	39.68 RPM
SRP017611_liver	0.04 RPM	28.77 RPM
SRP040447_lung	0.10 RPM	44.21 RPM
SRP040447_skeletal_muscle	0.03 RPM	40.70 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1052 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1052 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000027117	1 retrocopy	retro_cpor_1052 ,
Loxodonta africana	ENSLAFG00000015096	1 retrocopy	retro_lafr_466,