RetrogeneDB ID: retro_cpor_1420

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_8:49179635..49180487(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSG101
• Ensembl ID: ENSCPOG00000011994
• Aliases: None
• Description: None

Sequence

>retro_cpor_1420
ACTGTATGTGAAACTGTCAATGTTATTTCACTGTACAGAGATCACAAGTCTATATTGAATTCATATGTTTTGAATGAAGG
CAGTTCTAGGGAACTAATGAGCCTCACTGGAACAATTCCTGTGCCTTACAGATGTAATATGCATAATATGCCAACATGAC
TATGGCTGCTGGTTGCATACTTATATAATTCCCCTATCTGTTTTGTTAAGCCTACTAGTTCAATGATTATTAAAACAGGA
AAGCATGTTGATGCAAATGGGAAATTTTAAGTCCTTAACATGCATGAATAGAAAGAAACACCCTCAGTCAGACCTGCTGG
GACTTATTAATTCATGATTGTAGTGTTTGGAGATGAACTTCCTGTCTTCTCTTGTCCTGCTGTTTCAGCATCTTATCCAA
CATAGCAAGCAACAGGGCCACTAAATACCTCCTACATGCCAGGCATGCCTGGTGGAATCTCTGCATACCCATCTGGATAG
TCTCCTAATTGCAGTAATAACGCAGGGTGTCTTTACCCACCTGGTATCCATACTCTGTCACAACAGGCTCTCATTACCCT
TCTCAGCCTCATTTGACCACTATTGGTCCCTCATAGATGACACCATCAGTGAGGATACCATCTGGAGAGAGGATACCTCT
CTCTTTTTGGCAGTCAGTGACAAACTAAGATGGTGAATGAAGGAAGAGATGAATCATGCCCAGACAGAGCTTAATGCCTT
AAAATGAACAGAGGAAGAACTATAAAAAGAACACCAGGAACTGGAAGAAATTGTCACTCGTTTAAATCAAGAAGTAGCTG
GAGTTGATACAAATGTAGAACTTTATAAAAGAAGGATGAAGAACTCTTCTCT

Alignment

ORF - retro_cpor_1420 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.1 %
• Parental protein coverage: 71.87 %
• Number of stop codons detected: 9
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  TVRETVNVITLYKDLKPVLDSYVFNDGSSRELMNLTGTIPVPYRGNTYNIPICLWLLDTYPYNPPICFVK
          TV.ETVNVI.LY.D.K..L.SYV.N.GSSRELM.LTGTIPVPYR.N..N.P..LWLL..Y.YN.PICFVK
Retrocopy TVCETVNVISLYRDHKSILNSYVLNEGSSRELMSLTGTIPVPYRCNMHNMPT*LWLLVAYLYNSPICFVK

Parental  PTSSMTIKTGKHVDANGKIYLPYLHEWKH-PQSDLLGLIQVMIVVFGDEPPVFSRPTVSASYPPYQATGP
          PTSSM.IKTGKHVDANGK......HE.K..P.....G....MIVVFGDE.PVFS.P.VSASYP..QATGP
Retrocopy PTSSMIIKTGKHVDANGKF*VLNMHE*KETPSVRPAGTY*FMIVVFGDELPVFSCPAVSASYPT*QATGP

Parental  PNTSYMPGMPSGISAYPSGYPPNPSGYPGCPYPPG-GPYPATTSSQYPSQPPVTTVGPS-RDGTISEDTI
          .NTSYMPGMP.GISAYPSG..PN.S...GC.YPPG..PY..TT.S.YPSQP..TT.GPS..D.TISEDTI
Retrocopy LNTSYMPGMPGGISAYPSG*SPNCSNNAGCLYPPG<YPYSVTTGSHYPSQPHLTTIGPS<IDDTISEDTI

Parental  ---RASLISAVSDKLRWRMKEEMDRAQAELNALKRTEEDLKKGHQKLEEMVTRLDQEVAEVDKNIELLK-
          .....SL..AVSDKLRW.MKEEM..AQ.ELNALK.TEE.L.K.HQ.LEE.VTRL.QEVA.VD.N.EL.K.
Retrocopy WREDTSLFLAVSDKLRW*MKEEMNHAQTELNALK*TEEEL*KEHQELEEIVTRLNQEVAGVDTNVELYK<

Parental  KKDEELSS
          KKDEEL.S
Retrocopy KKDEELFS

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	31.35 RPM
SRP017611_kidney	0.00 RPM	63.75 RPM
SRP017611_liver	0.35 RPM	57.98 RPM
SRP040447_lung	0.00 RPM	36.82 RPM
SRP040447_skeletal_muscle	0.00 RPM	39.37 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1420 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1420 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 5 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013563	4 retrocopies	retro_btau_1009, retro_btau_698, retro_btau_825, retro_btau_979,
Canis familiaris	ENSCAFG00000009279	1 retrocopy	retro_cfam_1615,
Cavia porcellus	ENSCPOG00000011994	1 retrocopy	retro_cpor_1420 ,
Myotis lucifugus	ENSMLUG00000016353	2 retrocopies	retro_mluc_1133, retro_mluc_1713,
Mus musculus	ENSMUSG00000014402	1 retrocopy	retro_mmus_1350,