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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttttgaccttttgttgcaaattttgtgatcagtacttttgaaagtcatgctataattgttttggttaaccctgaccattgattgatgatggaa...

Basic information

species Oryza sativa
transcript LOC_Os01g64690.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA02G09090.1 (Glycine max), 5'ss of exon 2
GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttttgaccttttgtt--gcaaattttgtgatcagtacttttgaaagtc--atgctataattgttttggttaaccctgaccattgattgatgatggaa
|| || ||||| ||| | || ||||||||||| |||||||| || ||| | || ||||| || || || ||||||||||| |||||||||||| | ||||||  |   | |  |   |  |  || |      | | |  ||   ||||    ||| || || |||      |  |    |   || | | ||  | |  
GCTTATGATCAGCATCTTAATATGATTCTTGGCGATGTTGAAGAAATCATTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagt--tggaatcagtaactaagagaaatacacatttattttttggcaaagcttaatggtagaaatgtgaataattgctggaaattttaaataattttag--

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GLYMA16G28300.1 (Glycine max), 5'ss of exon 2
GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagt-gttttgaccttttgttgcaaattttgtgatcagtacttttga---aagtcatgctataattgttttggttaaccctgacca--ttgattgatgatggaa
|| || ||||| ||| | || ||||||||||| |||||||| || || || || ||||| || || || ||||||||||| |||||||||||| | |||||| ||  | | |   |   |  || |   |  | | |  ||||     |||  |     ||    | |   | |   |||   |  |||| | ||       
GCTTATGATCAGCATCTTAATATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTGGAAATCGATGATGAGACATACGAAGAAATTGTGAGGgtaagttgtaatcagcaactaa-gagaaatacatatttattcttttttggctaagctaaatggtagaaatgtgaataattgctggaaaatttgaataattt-----

upper sequence: LOC_Os01g64690.1 (Oryza sativa), 5'ss of exon 2
lower sequence: Vv18s0072g00710.t01 (Vitis vinifera), 5'ss of exon 2
GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt---tgaccttttgttgcaaattttgtga-tcagtacttttgaaagtcatgctataattgttttggttaac---cctgaccattgattgatgatggaa-----------------------------------------------------------------------------------
|| || ||||| ||||| |||||||||||||| |||||||| || || || || ||||| || || |||||||| || |||||||||||||| || ||| |   |    || | |  | || |   |||  | | | |     ||||  ||   ||  | |||      | |  ||   | | | |||   |  |  |    |                                                                                   
GCCTATGATCAGCATTTGAACATGATTCTTGGTGATGTTGAAGAAATTGTTACTACAGTAGAAATCGACGATGAAACTTATGAAGAAATTGTTCGAgtatgctctcaactggcttccttttacttctttcttaaattatctggtttggtagaactgaaacaatccagaagatccactggcataaacataactgcaccaccacaagccccaatcccccaccctgctgagaggaattaaataaataagcataacaagaatgtttctggaatttttttttttttgatag

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|88552429|gb|CI482435.1|CI482435
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88506337|gb|CI433843.1|CI433843
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88529735|gb|CI458076.1|CI458076
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|89163418|gb|CI100308.1|CI100308
EST:     TCGTGACAACAGTTGAGATGGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88471442|gb|CI408713.1|CI408713
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88521712|gb|CI448379.1|CI448379
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|8528361|gb|AU093176.1|AU093176
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGNAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88554838|gb|CI485047.1|CI485047
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88523672|gb|CI451520.1|CI451520
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88994793|gb|CI036374.1|CI036374
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88560752|gb|CI491445.1|CI491445
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88547915|gb|CI478246.1|CI478246
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|12622952|gb|AU173165.1|AU173165
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88526966|gb|CI455068.1|CI455068
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|25800894|gb|CA756855.1|CA756855
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88529062|gb|CI456389.1|CI456389
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88266873|gb|CI368649.1|CI368649
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|86530098|gb|CI170304.1|CI170304
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|86432320|gb|CI085931.1|CI085931
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|86418840|gb|CI053641.1|CI053641
EST:     TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: TCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
EST: gi|88543350|gb|CI473350.1|CI473350
EST:     GTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGC                         ACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT
genomic: GTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 75 (upstream exon), 32 (downstream exon)
Score: 14

GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttt ... ctttttccagACCACAAAACGCACTATCCCCTTCCTTTTTGTTCGAGGTGATGGTGTCATTTTGGTTTCTCCACCCCTCCGAACGGCATGAAGTATGAAGGAAGCTCCTG




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATACGATCAACATTTAAACATGATTCTTGGAGATGTTGAGGAGATCGTGACAACAGTTGAGATTGACGATGAGACATATGAAGAAATTGTGCGCgtaagtgttttgaccttttgttgcaaattttgtgatcagtacttttgaaagtcatgctataattgttttggttaaccctgaccattgattgatgatggaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA