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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attctggttcttttgaacttcgaagttgaatggattcaaaaccattctcgtgatacagttaagttagcatgtgcatctttcttacatcttgcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTTAATGGGCTGACCCCCGAGGTATGGCAGCTTGGTGCTGTTGGTGCGGTGA

Basic information

species Oryza sativa
transcript LOC_Os01g09120.2
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g09120.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G176506_T04 (Zea mays), 3'ss of exon 6
-------------------------------------------------------------------attctggttcttttgaacttcgaagttgaatggattcaaa-------accattctcgtgataca-----gttaagttagcatgtgcatctttctt----------acatcttgcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTTAATGGGCTGACCCCCGAGGTATGGCAGCTTGGTGCTGTTGGTGCGGTGA
                                                                     | ||   || |  |||| || |   |||| ||||   |       | || ||   |  | |      ||  |   | |||| | || ||| ||          || || | |||  |||||| || |||||  | ||||||||||||||   |||||||||| | ||||||| ||||||||||||||||  ||||| |||||| ||||||||||||||||
gtcttccctgaaagaaactgtctctcaaatgcattaaacaatcactacacaattgctatgtttgtgtgctatgaagctct-aaactacggaacagaatagatttgcagtttgctatcagtcagatattccgctcttgtacaaccatcatggggattttttttttcccgactgacttcatacctacgcagGTGGCCTTTCATATCTGGGTTCACCTTGACATGGGTGCAAAGCACGATTTTAGTGGGCTGACCCCCGAGAAATGGCTGCTTGGCGCTGTTGGTGCGGTGA

upper sequence: LOC_Os01g09120.2 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G176506_T07 (Zea mays), 3'ss of exon 6
-attctggttcttttgaacttcgaagttgaatggattcaaaaccattctcgtgatacagttaagttagcatgtgcatcttt--cttacatcttgcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTTAATGGGCTGACCCCCGAGGTATGGCAGCTTGGTGCTGTTGGTGCGGTGA
 |      |   |||| | || |   |      |||   |  ||  ||| ||   ||  | | |      | |   |      || || || | |||  |||||| || |||||  | ||||||||||||||   |||||||||| | ||||||| ||||||||||||||||  ||||| |||||| ||||||||||||||||
gaacagaatagatttgcagtttgctatcagtcagat---attccgctcttgtacaaccatcatggggattttttttttcccgactgacttcatacctacgcagGTGGCCTTTCATATCTGGGTTCACCTTGACATGGGTGCAAAGCACGATTTTAGTGGGCTGACCCCCGAGAAATGGCTGCTTGGCGCTGTTGGTGCGGTGA
















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|29660689|gb|CB656964.1|CB656964
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|29660992|gb|CB657267.1|CB657267
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|88221282|gb|CI221238.1|CI221238
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|86505958|gb|CI148591.1|CI148591
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|29657673|gb|CB653948.1|CB653948
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAAGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|29680769|gb|CB677044.1|CB677044
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|88966127|gb|CI013003.1|CI013003
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|29662742|gb|CB659017.1|CB659017
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|86527492|gb|CI167698.1|CI167698
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|88461305|gb|CI547485.1|CI547485
EST:     CGTTCCGTGGTCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|87027196|gb|CI278228.1|CI278228
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|31818552|gb|CD645551.1|CD645551
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCGTCGGGCGAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|29640574|gb|CB645583.1|CB645583
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|29655805|gb|CB652080.1|CB652080
EST:     CGTTCCGTGATCTTGTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCCTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|14571448|gb|BI118816.1|BI118816
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCGTCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|38474285|gb|CF958417.1|CF958417
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCGTCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTG
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTG
EST: gi|86869605|gb|CI322091.1|CI322091
EST:     CGTTCCATTATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTG-AGGTTCACCTTGATGAGGGGTGCAAAGTATGATTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGA-GGGTGCAAAGTATGATTT
EST: gi|88228766|gb|CI228246.1|CI228246
EST:     CGTTCCGTGATCTTCTACATATATTTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|29660961|gb|CB657236.1|CB657236
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCCCCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT
EST: gi|29638115|gb|CB643124.1|CB643124
EST:     CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAG                         GTAGCATTTCACGTGTGGGTTCCCCTTGATGAGGGTGCAAAGTATGATTTT
genomic: CGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTT

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), 51 (downstream exon)
Score: 10

GAAAGGTGGAAGCTCGTTCCGTGATCTTCTACATATATCTCCTATACGAAATGCATCGGGCAAGgttcgttttc ... gcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTTAATGGGCTGACCCCCGAGGTATGGCAGCTTGGTGCTGTTGGTGCGGTGA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctcgtgatacagttaagttagcatgtgcatctttcttacatcttgcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTTAATGGGCTGACCCCCGAGGTATGGCAGCTTGGTGCTGTTGGTGCGGTGA
                                 ttcttac  putative branch site (score: 10)
                                         tcttgcct  CT-rich tract
             ttaagtta  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attctggttcttttgaacttcgaagttgaatggattcaaaaccattctcgtgatacagttaagttagcatgtgcatctttcttacatcttgcctgtgcagGTAGCATTTCACGTGTGGGTTCACCTTGATGAGGGTGCAAAGTATGATTTTAATGGGCTGACCCCCGAGGTATGGCAGCTTGGTGCTGTTGGTGCGGTGA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- -ctggttc
- - - - - - - - - - - - - tgaatgg
- - - - - - - - - - - - - - - - - - - aaaccat
- - - - - - - - - - - - - - - - - - - - - - - - - tgataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgc