RetrogeneDB ID: retro_mmus_1379

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 15:3217491..3218749(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: Ewsr1
• Ensembl ID: ENSMUSG00000009079
• Aliases: Ewsr1, Ews, Ewsh
• Description: Ewing sarcoma breakpoint region 1 [Source:MGI Symbol;Acc:MGI:99960]

Sequence

>retro_mmus_1379
CAACCTCAATCTAGCACAGGGGGTTATAACCAACCCAGCCTAGGATATGGACAGAGTAACTTCAGTTACAATCAGAGCAG
TTACTCTCAGCAGAACACCTATGGGCAGCCGAGCAGCTATGGACAGCAGCGTAGCTATATGGTCAACAAAGCAGATATGG
GTAGCAGCCTCCTACTAGTTACCCCCCTCAGACTGGATCCTACAGCCAGGCTCCAAGTCATTATAGCCAACAGAGCAGCA
GCTAGGGGCAGCAGAGTTCATTCCAACAGGACCACTCCAGTAGCATGGGTGTTTATGGGCAAGAGTCTGGAGGATTTTCC
GGACCAGGAGAAAACCGGAGCTTAAGTGGCCCTGATAACCGGGGCAGGGGAAGAGGGGAATTTGATCGTGGGGGCATGAG
CAGAGGTGGGTGGGGAGGAAGCAAGTTGGAATGGGCGCTGGAGAGCAAGGTGGCTTCAATAAGCCTGATGGACCCATGGA
TGAAGGACCAGATCTTGATCTAGGCCTTCCTATAGATCCCGATGAAGACTCTGACAACAGTGCAATTTATGTGCAAGGAT
TAAATGACAATGTGACTCTGGATGATCTGGTAGACTTCTTTAAGCAGTGTGGGGTTGTCAAGATGAACAAGAGAACTGGA
CAACTCATGATCCATATCTACATGGATAAGGAGACAGGAAGGCCTAAAGGTGATGCCACAGTGTCTTATGAAGATCCACC
AACTGCCAAGGCTGCCGTGGAATGGTTTGATGGGAAAGATTTTCAAGGAAGCAAACTTAAAGTTTCTCTTGCCCGAAAGA
AGCCTCCAATGAACAGCACGGGGGGTGGCATGCCACCACGTGAGGGCAGAGGGATACCACCACCACTTCGTGGAGGTCCT
GGTGGCCCAGGAGGCCCTGGAGGACCCATGGGTCACATGGGAGGCCGTGGAGGAGACAGAGGGGGCTTCCCTCCAAGAGG
GCCCGGAGGCTCCAGAAGAAACCCCTCTGGCGGAGGAAATGTCCAGCATCGAGCTGGAGACTGGCAGTGTCCAATTCCGG
ACTGTAGAAACCAGAACTTCGCTTGGAGAACAGAATGCAACCAGTGTAAGGCCCCTAAGCCCGAGGGCTTCCACCCGCGA
TCGTGGACGAGGTGAGGGGGAAGAGGACTCATGGACCGTGGTAGTCCTGGAGGAATGTTCAGAGGTGGCAGAGGTGGAGA
CAAAGGAGGCTTCCGAGGTGGCCGTGGAATGGACCAAGGTTGGTGGAGGAAGACGAGG

Alignment

ORF - retro_mmus_1379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.24 %
• Parental protein coverage: 63.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QPVTAPPSYPPTSYSSSQPT-SYDQSSYSQQNTYGQPSSYG-QQSS-YGQQSSYGQQPPTSYPPQTGSYS
          QP......Y...S....Q...SY.QSSYSQQNTYGQPSSYG.Q.S..YGQQS.YG.QPPTSYPPQTGSYS
Retrocopy QPQSSTGGYNQPSLGYGQSNFSYNQSSYSQQNTYGQPSSYGQQRSY<YGQQSRYG*QPPTSYPPQTGSYS

Parental  QAPSQYSQQSSSYGQQSSFRQDHPSSMGVYGQESGGFSGPGENRSLSGPDNRGRGRGGFDRGGMSRGGRG
          QAPS.YSQQSSS.GQQSSF.QDH.SSMGVYGQESGGFSGPGENRSLSGPDNRGRGRG.FDRGGMSRGG.G
Retrocopy QAPSHYSQQSSS*GQQSSFQQDHSSSMGVYGQESGGFSGPGENRSLSGPDNRGRGRGEFDRGGMSRGGWG

Parental  GGR-GGLGAGERGGFNKPGGPMDEGPDLDLGLPIDPDEDSDNSAIYVQGLNDNVTLDDLADFFKQCGVVK
          G....G.GAGE.GGFNKP.GPMDEGPDLDLGLPIDPDEDSDNSAIYVQGLNDNVTLDDL.DFFKQCGVVK
Retrocopy GSK<VGMGAGEQGGFNKPDGPMDEGPDLDLGLPIDPDEDSDNSAIYVQGLNDNVTLDDLVDFFKQCGVVK

Parental  MNKRTGQPMIHIYLDKETGKPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSMRGGM
          MNKRTGQ.MIHIY.DKETG.PKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNS..GGM
Retrocopy MNKRTGQLMIHIYMDKETGRPKGDATVSYEDPPTAKAAVEWFDGKDFQGSKLKVSLARKKPPMNSTGGGM

Parental  PPREGRGMPPPLRGGPGGPGGPGGPMGRMGGRGGDRGGFPPRGPRGSRGNPSGGGNVQHRAGDWQCPNPG
          PPREGRG.PPPLRGGPGGPGGPGGPMG.MGGRGGDRGGFPPRGP.GSR.NPSGGGNVQHRAGDWQCP.P.
Retrocopy PPREGRGIPPPLRGGPGGPGGPGGPMGHMGGRGGDRGGFPPRGPGGSRRNPSGGGNVQHRAGDWQCPIPD

Parental  CGNQNFAWRTECNQCKAPKPEGFLPPPFPPPGGD--RGRGGPGGM-RGGRGGLMDRGGPGGMFRGGRGGD
          C.NQNFAWRTECNQCKAPKPEGF.P......GG.....RG.PGGM.RGGRGG..D.GG....FRGGRG.D
Retrocopy CRNQNFAWRTECNQCKAPKPEGFHPRSWTR*GGRGLMDRGSPGGMFRGGRGG--DKGG----FRGGRGMD

Parental  RGGFRGGR
          .G..R..R
Retrocopy QGWWRKTR

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
SRP007412_brain	0.09 RPM	167.37 RPM
SRP007412_cerebellum	0.13 RPM	225.62 RPM
SRP007412_heart	0.22 RPM	108.18 RPM
SRP007412_kidney	0.21 RPM	158.02 RPM
SRP007412_liver	0.03 RPM	84.96 RPM
SRP007412_testis	0.87 RPM	353.52 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_1379 was not detected

EST

No EST(s) were mapped for retro_mmus_1379 retrocopy.

TSS

No TSS is located nearby retro_mmus_1379 retrocopy 5' end.

Lab

retro_mmus_1379 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_1379 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008298	2 retrocopies	retro_amel_191, retro_amel_959,
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,
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,
Mus musculus	ENSMUSG00000009079	1 retrocopy	retro_mmus_1379 ,
Mus musculus	ENSMUSG00000030795	2 retrocopies	retro_mmus_2710, retro_mmus_2952,
Oryctolagus cuniculus	ENSOCUG00000004432	2 retrocopies	retro_ocun_1346, retro_ocun_242,
Ictidomys tridecemlineatus	ENSSTOG00000023177	1 retrocopy	retro_itri_1892,