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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG

Basic information

species Zea mays
transcript GRMZM2G082484_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 3'ss of exon 3
----------tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
           | | |     || | |   |||   |    | | ||| | | || || |  | || |  | ||      ||    |||  ||||| |    ||  | |||||||||| ||||||||||||| |||||||| ||||| ||||||||||| ||||| |||||||| |||||||||||||| ||||| ||||||||||||||
ataaaatttaagttactgccttgttttacagatgttacaatacacaaaaactgtcattatgttctctcgtaatt------tgtttcttgatatttttt----gtcaatagGTATTGTCTTGGATTCTGGAGATGGTGTCAGTCACACAGTCCCAATCTACGAAGGTTATGCCCTTCCGCATGCCATTCTCCGTCTTGATCTTGCTGGTAG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA15G05570.1 (Glycine max), 3'ss of exon 3
-tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttga-cagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
 | |  ||   |  | |  |||||| | ||| ||     ||  ||  || | |      | | || || | ||     |    || ||||    || | |||||||||| || |||||||| || ||||| |||||||| || || || |||||||| ||||| || || ||||| ||||||||  | || ||||||||  |
attccacacgtacaagagtgggatatacatgcattt--ctacattaattatgaccagcattatttccttattggtttgtcttgttatgttggtattaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACGGTGCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G19420.1 (Glycine max), 3'ss of exon 3
tgctgcataaatgatatggggatagaaatggatagaaatatt--ttcctttttatttcactcagttgctcaatg-cacattgggattttgttttggttga-cagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
     |||| |    |  |||||| | ||| ||    | |||  |||||    |      | | || || | |  |   |     || ||||    || | |||||||||| || |||||||| || ||||| |||||||| || || || |||||||| ||||| || || ||||| ||||||||  | || ||||||||  |
----acatatacatgagtgggatatacatgtatttccacattaattcctcacgaccagtattatttccttattttcttgtctttgttatgttggcattaaacagGTATTGTGCTTGATTCTGGTGATGGTGTGAGCCACACAGTTCCCATATATGAAGGGTATGCTCTTCCTCATGCAATTCTTCGGTTGGACCTTGCTGGCCG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA08G15480.1 (Glycine max), 3'ss of exon 3
tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
              | ||   ||    ||   |    ||   ||| ||| || |    |   |   ||  || |       | ||  ||||     |||||||||||  |||| ||||| || ||||| || |||||||| ||||||||||| || ||||| ||||| |||||||| |||||| | ||||| |||||| |
-------------gtttgtatatcaccatctgtcttgattcattcttttataatcacattgttctttccctgaatc-----aattccttttaa--aacagGTATTGTATTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCTGGTCG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA05G32220.1 (Glycine max), 3'ss of exon 2
tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
              | ||   ||    ||   |    ||   ||| ||| || |    ||| |   ||  || |       | ||  |||      |||||||||||  |||| ||||| || ||||| || |||||||| ||||||||||| || ||||| ||||| |||||||| |||||| | ||||| || ||| |
-------------gtttgtatattaccatctgtcttgattcattcttttataatcacatcattctttccctgaatc-----aattcctttcaa--aacagGTATTGTGTTGGACTCTGGTGATGGTGTGAGTCACACTGTACCAATCTATGAGGGGTATGCACTCCCCCATGCCATCCTTCGTTTGGATCTCGCAGGTCG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA04G39380.2 (Glycine max), 3'ss of exon 3
tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
                |  | ||    ||  ||     |   ||| |  || | |||     ||| ||  | |        | |   || ||    |||||||||||  |||| ||||| || ||||| || |||||||| ||||||||||| |||||||| ||||| ||||||||||||||| | |||||||||||  |
---------------gtttgtatttgtatccatctgtttcaattcatagttttgtcatcacattgttctttccctgaatcaaatactttctga--aacagGTATTGTTTTGGACTCTGGCGATGGTGTTAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTTCGTTTGGATCTTGCTGGCCG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 3
tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
              | |    ||    ||   |   |||    |||||| |  |||||    ||| || || |        | | | |||   |   ||||||||||  |||| ||||| || ||||| || |||||||| ||||||||||| |||||||| ||||| ||||||||||| ||| | |||||||||||  |
-----------gtttgtacttatttccatctgtcttaattcactcctttgt-cttcac---attgttctatccttgaatcaaatctttttgaat---cagGTATTGTTTTGGACTCTGGTGATGGTGTGAGTCACACTGTGCCAATCTATGAGGGCTATGCACTCCCTCATGCCATTCTCCGTTTGGATCTTGCTGGCCG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 3
tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
 | |   |      | |    ||  || |    ||  ||||| || | ||  ||  | | | ||         |  | |   || | |||| ||  ||||||||||| || |||||||| || |||||    |||||||| |||||||| || || ||||| || || ||||| || |||||||| |||||||| ||| |
-gttagttcttaactctaaacatccaagtctg-agttatattatcttcttacttgtatttactta--------aagtcg---ttctctttttgt-aacagGTATTGTGCTCGATTCTGGTGATGGTGTGTCTCACACTGTGCCAATCTACGAGGGGTATGCTCTTCCTCATGCTATCCTTCGTCTTGATCTTGCGGGTCG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 4
tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgac-agGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
           |  |||    ||     ||||| | ||| |||   ||||  ||||  |   | |   |       ||   | ||  |  |  ||||| ||||||||| ||||||||||| || ||||| || |||||||| ||||| |||||||| ||||| || || ||||| || |||||||| || ||||||||  |
---------gttcgtattaaaatctttttggattggaat-tttcatttttcttttctgttgttagtgtagcctgagttctaacttgctcct--ttgactagGTATTGTGCTGGATTCTGGTGATGGTGTGAGTCACACTGTGCCAATTTATGAAGGTTATGCACTTCCCCATGCTATCCTTCGTCTTGACCTTGCTGGACG

upper sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 3
lower sequence: Vv12s0178g00200.t01 (Vitis vinifera), 3'ss of exon 2
-tgctgcataaatgatatgggga-tagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttg-gttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
    | ||  |||  | |    | ||    |   |    |   |    || ||||     ||  ||| |  ||    | ||   |||| |  || ||  | |||||||||| |||||||||| || ||||||||||| || || |||||||||||||| ||||| || || ||||| || |||||  | || ||||||||| |
aaatttcaagaattttttcctcagtattggtaactgccgactatgattttcttatcctgttct-ttgtt--atatttactgaagttttttggtgtgtgaaaagGTATTGTCTTGGATTCTGGTGATGGTGTCAGCCATACAGTGCCAATCTATGAAGGATATGCTCTTCCACATGCAATCCTTCGATTAGACCTTGCTGGTCG

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|14204329|gb|BG838006.1|BG838006
EST:     GTTGCTATTCAAGCTGTCHTTYCCCTTTATGCTAGTGGCCGTACCCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTAT
genomic: GTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTA-CCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTAT
EST: gi|31353490|gb|CD437847.1|CD437847
EST:     TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
genomic: TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
EST: gi|211240566|gb|FL158540.1|FL158540
EST:     TGTTGCTATTCAAGCTGTCCTTTCCCTATATGCTAGTGGCCGTACCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGTCACACTGTCCCAATCTATG
genomic: TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
EST: gi|31354996|gb|CD439353.1|CD439353
EST:     TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
genomic: TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
EST: gi|211242789|gb|FL158545.1|FL158545
EST:     TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
genomic: TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
EST: gi|211242785|gb|FL158541.1|FL158541
EST:     TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
genomic: TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
EST: gi|31355598|gb|CD439955.1|CD439955
EST:     TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
genomic: TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
EST: gi|211245024|gb|FL158556.1|FL158556
EST:     TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCC
genomic: TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCC
EST: gi|78083306|gb|DV511699.1|DV511699
EST:     TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTG                         GTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG
genomic: TGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATG

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 4 RNA-Seq libraries.


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 187

GAAAAGATGACACAAATCATGTTTGAAACTTTCAGTGTTCCTGCTATGTATGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 167

GAAAAGATGACACAAATCATGTTTGAAACTTTCAGTGTTCCTGCTATGTATGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 146

GAAAAGATGACACAAATCATGTTTGAAACTTTCAGTGTTCCTGCTATGTATGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 156

GAAAAGATGACACAAATCATGTTTGAAACTTTCAGTGTTCCTGCTATGTATGTTGCTATTCAAGCTGTCCTTTCCCTTTATGCTAGTGGCCGTACCACTGgtaagtgatc ... tggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG
                                     ttttgtttt  CT-rich tract
                                    attttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgctgcataaatgatatggggatagaaatggatagaaatattttcctttttatttcactcagttgctcaatgcacattgggattttgttttggttgacagGTATTGTCCTGGATTCTGGAGACGGTGTCAGCCACACTGTCCCAATCTATGAAGGCTATGCCCTCCCGCATGCCATTCTTCGTCTCGATCTTGCTGGTAG

tgctgca
- - - - - - - - - - gatagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttttgtt