RetrogeneDB ID: retro_cpor_1353

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_71:8518792..8519898(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EWSR1
• Ensembl ID: ENSCPOG00000009502
• Aliases: None
• Description: None

Sequence

>retro_cpor_1353
TCAACAAAGCAGCCATGGGCAGCAGCCTCCCACTAGTTATCTCCCTCTGCCCAAGCTGGATCCTGCAGCTAGCCTCCAAG
TCAATATAGCCAACAGAGCAGCAGCTACAGGCAGCAGAGTTCATTCTGACAGGACTACCCCAATAGCCTCAGTGTTTATG
GGCAGGAATATGGAGGATTTTCCAGATCAGGAGAGAACTGGAGCATGAGTGGCCCTGATAACCAGGGCAGGGAAAGAGGG
GGATTTGCTCATGGAAGCATGAGCAGAGATGGGTGGGAAGGAGGACACAGTGGAATGGGCAGCGATAGAGAGTAGGTGGC
TTCAGTAAGAATGGTGGATCCACGGATGAAGGACCAGATCTTGATCTAGGCCCTCCCATACATCCTGAGGAAAGATCTGA
CAACAGTGCAATTTATGTACAAGGATTAAATGACAGTGTAACACTCAATGACCTGGCAGACTTCTTTAAGCAATGTGGGG
TTGTTAAGATTAAAGAAGAGAACCAGGCAACCCATGATCCACATCTACCTGGACAAGGAAACAGAAAAGCCCAAAGTTGA
TGCCACGGTGTCCTAGGAAAATCCACAGACTTCCAAGGCTGCTATGGAGTGGTTTGATGAGAAAGATTTTCAAGAAAGCA
AACTTAAGTTTCCTGTTCAGAAGAAGCTCAATGAACAGTATGTGAAGTAGCATGTCACCCCATGAAGGCAGAAGGGTGCA
TCACCATGCCTTGGAAGTCCAGGTGGGAGAGGGCGGTGGGGGACCCACATATCACATAAGAGGCTGCAGAACAGACAGGT
AAGGCTTCCCTCCAAAAGGCCTCTGAGGTTCCCCAAGAAACCCCTCTGAAGGAAGAAACATCTAACATCGAGCTGGAGAT
TCACATTTTCCCAATCCGGGTTGTGGAAATCAGAACTTCACCTGAAGAGCACAATGCAACCAGTCAGTGTAAGGCCCTGA
AATCTAAAGGCTTCCTCCCACCACCCTACCCACCCCCAGGTGGTGATCGTGGGAGAAGTGGTACTGATGGCATATTGGGA
GGAAGAGATTGCCTCATGGACAGTGGTGGTCCTGGTGGAATGTTCAGAGGTGGCCATAACGGAGAC

Alignment

ORF - retro_cpor_1353 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.79 %
• Parental protein coverage: 59.3 %
• Number of stop codons detected: 12
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  SSTQPTSYDQSSYSPTSYPPQTGSYSQAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENR
          S..QP........SP.....Q.GS.S..PSQYSQQSSSY.QQSSF.QD.P.S..VYGQE.GGFS..GEN.
Retrocopy STKQPWAAASH*LSPSA---QAGSCS*PPSQYSQQSSSYRQQSSF*QDYPNSLSVYGQEYGGFSRSGENW

Parental  SMSGPDNRGRGRGGFDRGGMSRGGRGGGRGGMGSAGE-RGGFNKPGGPMDEGPDLDLGPPIDPDEDSDNS
          SMSGPDN.GR.RGGF..G.MSR.G..GG..GMGS..E..GGF.K.GG..DEGPDLDLGPPI.P.E.SDNS
Retrocopy SMSGPDNQGRERGGFAHGSMSRDGWEGGHSGMGSDRE<VGGFSKNGGSTDEGPDLDLGPPIHPEERSDNS

Parental  AIYVQGLNDNVTLDDLTDFFKQCGVVKI-NKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVDWF
          AIYVQGLND.VTL.DL.DFFKQCGVVKI..KRT.QPMIHIYLDKET.KPK.DATVS.E.P.T.KAA..WF
Retrocopy AIYVQGLNDSVTLNDLADFFKQCGVVKI>KKRTRQPMIHIYLDKETEKPKVDATVS*ENPQTSKAAMEWF

Parental  DGKDFQGSKLKVSLARKKPPMNSMRGGMPPREGRGMPPPLRGGPG-GPGGPGGPMGRMGGRGGDRGGFPP
          D.KDFQ.SKLK.....KK...........P....G..P.L.G.PG.G.GG.G.P.....G...DR.GFPP
Retrocopy DEKDFQESKLKFPV-QKKLNEQYVK*HVTP*RQKGASPCL-GSPG>GEGGGG-PTYHIRGCRTDR*GFPP

Parental  RGPRGSRGNPSGGGNVQHRAGDWQCPNPYVFSLLIAWRTECNQCK-APKPEGFLPPPFPPP-GGDRGRGG
          .G..GS..NPS.G.N..HRAGD...PNP.........R..CNQ....P......P...P.P.GGDRGR.G
Retrocopy KGL*GSPRNPSEGRNI*HRAGDSHFPNPGCGNQNFT*RAQCNQSV*GPEI*RLPPTTLPTP>GGDRGRSG

Parental  PGGMRGGRGGLMDRGGPGGMFRGGRGGD
          ..G..GGR..LMD.GGPGGMFRGG..GD
Retrocopy TDGILGGRDCLMDSGGPGGMFRGGHNGD

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	128.43 RPM
SRP017611_kidney	0.00 RPM	171.90 RPM
SRP017611_liver	0.00 RPM	83.96 RPM
SRP040447_lung	0.00 RPM	212.66 RPM
SRP040447_skeletal_muscle	0.00 RPM	71.17 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_1353 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_1353 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 10 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012160	8 retrocopies	retro_cfam_1142, retro_cfam_1183, retro_cfam_1225, retro_cfam_133, retro_cfam_1397, retro_cfam_1736, retro_cfam_1889, retro_cfam_560,
Callithrix jacchus	ENSCJAG00000019987	4 retrocopies	retro_cjac_1716, retro_cjac_2022, retro_cjac_2813, retro_cjac_2911,
Cavia porcellus	ENSCPOG00000009502	1 retrocopy	retro_cpor_1353 ,
Felis catus	ENSFCAG00000004243	1 retrocopy	retro_fcat_519,
Macropus eugenii	ENSMEUG00000008703	1 retrocopy	retro_meug_1424,
Myotis lucifugus	ENSMLUG00000012058	1 retrocopy	retro_mluc_328,
Monodelphis domestica	ENSMODG00000008679	1 retrocopy	retro_mdom_279,
Mustela putorius furo	ENSMPUG00000013432	2 retrocopies	retro_mputfur_56, retro_mputfur_572,
Oryctolagus cuniculus	ENSOCUG00000004432	2 retrocopies	retro_ocun_1346, retro_ocun_242,
Ictidomys tridecemlineatus	ENSSTOG00000023177	1 retrocopy	retro_itri_1892,