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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

Basic information

species Zea mays
transcript GRMZM2G459746_T01
intron # 13
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: LOC_Os02g31290.1 (Oryza sativa), 3'ss of exon 13
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                                                      | |||| |  | ||  |  ||  | |||| ||| |||| || ||| || | |||||   ||||| ||  |    | ||  || ||| |  |  | | |||| ||||| || ||||| || |||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||||| ||||||| |||||||| ||||
---------------------------------------------------ggcaatagcttacgttctgc--atgcggcttgtcaactttggacattg-tacattatccaatttgaa-ataaat---caatattgtgccctcatccc-ttttttgcagACGTTCAATGGCAAGAAGTGGGAAAAGTTTAACAGTGAGAAAGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAATCAGCTCTTATTGCTCACTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G01040.1 (Glycine max), 3'ss of exon 13
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                                                          |   || |     |  ||||| |||    || | |    | || || | |  |      |  | || |       || |   |    |  || |||| ||| ||||| |||| ||||| |||||||||||||| ||||| || || || |||||||| |||||  |||| ||||| |||    |||| |||||||||||||
----------------------------------------------------------gttgtttggattttcttatgctttgagctatctatgtact-atgaattttgggttcctcatgttgatggaa----ctaaataaa---gaaatgttttgcagGCTTTTGATGGGAAAAAATGGGAGAAGTTTAATAGTGAAAAAGTAGCCTCACTTGCCTATGCCCGAATTCAAGGAAAAGGTTCTCTTATTGCTCATTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA08G28860.1 (Glycine max), 3'ss of exon 5
gtcagaaaattattccaattgacgaagtgctactgcat-tgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgt-catctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                           |||||  | |  |||||   |     ||| |      || | ||||||||   |     | |||   ||    |    | |     | || ||       |  ||  ||||  | | |  | ||  | |  |||   ||  |||| || || |||||||| || ||||||||||| ||||||||||| || |||||| | || ||||||||| ||||||| |||||||| ||||
------------------------gtctgctatggaaaatgatgatgacaatcaaaatgattgctgttaaacttata-atcacataacattcacacacacac---acacataccctgtac-------taatagactgaagcttatgatgcaattctggcagGTGTTCGATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGTATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA18G51690.1 (Glycine max), 3'ss of exon 4
gtcagaaaattattccaattgacgaagtgctac-tgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                           |||||     | |||||   |     ||| |      || | ||||||||   |     | |||   |    || | |       || |  |||  |   |  ||  || |   ||  || ||| | |  |||   || ||||| || || |||||||| || ||||||||||| ||||||||||| || |||||| | || ||||||||| ||||||| |||||||| ||||
------------------------gtatgctatacaaaatgatgatgacaatgaaaatgattgctgttaaacttata-atcacataacattcaca----gacacac------gcatacacactgtactaatagactaacttatgatg-catttctggcagGTGTTCAATGGGAAGAAATGGGAGAAATTCAACAGTGAGAAAGTGGCATCACTAGCATATGCTCGCATACAAGGGAAAGCAGCTCTCATTGCTCACTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: GLYMA04G37810.2 (Glycine max), 3'ss of exon 9
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaa-actagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                                 |   | ||        ||||| ||||   |||| |  | |||| ||   |   || | ||   |    | |    |   | ||   |   ||  || |||    |     |  |  || || | ||| ||||| |||| ||||| ||||||||||| |||||||| ||||| |||  ||| || |||||  |||| ||||| ||| | ||||| |||||||||||||
-------------------------------gttatttggaaacccttatgtaatactaa--tttgatataattatctgtgatttgaattctgagttcatctgattctttttgttt---ctaagagttgatatatctaatagataaggaatattgtacagGCTTTTCATGGGAAAAAATGGGAGAAGTTCAACAGTGAAAAGGTAGCAGTACTCGCCTATGCCCGAATTCAAGGAAAATCTGCTCTTATTGCTCATTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT5G61960.2 (Arabidopsis thaliana), 3'ss of exon 12
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                                                                          ||     |   |    ||   |||  ||     |  | | |       ||            |||  ||     | | ||  ||| | |||||||| ||||||||||| ||||| || || |||||||||||| | ||| | |||||| | |||||||||||||||||||| ||||| |||||||
-------------------------------------------------------------------------gtacagtctcatattgctgctttttcttatggcttttgtccttttgggagagcattggctaaaagctcttaaaaaaacattcacagGCATTTAATGGCAAAAAGTGGGAAAAGTTCAATAGCGAGAAGGTGGCAACGCTTACGTATGCTCGTATCCAAGGGAAAACAGCTCTTATTGCCCATTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: AT5G07290.1 (Arabidopsis thaliana), 3'ss of exon 12
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaat-ttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                                         | ||| | | |  ||     | || |||| || | |   |     |   |||| ||||   |||| |        | | |    |||    |    ||     ||   | | ||  ||| | || || ||||| || ||||| ||||| ||||| |||||||||||||| ||||| |||| | | || || |||||| ||||||| ||||| |||||||
----------------------------------------gtataa-gctttgtacctttttatgatcaatttgtgtagatgatgtatcattgttctttagaaaaaaa--------ggaaaaaagcgtttggttacaag-----tttaaaaccttaacagGCATTCAACGGTAAGAAATGGGAAAAGTTCAACAGCGAGAAGGTGGCATCGCTTGCATATGGTCGGATTCAGGGGAAATCAGCTCTTATTGCCCATTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv17s0000g00240.t01 (Vitis vinifera), 3'ss of exon 13
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggct----tgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
            ||  |||  | | | || || |  | | ||    | |  |    | | ||||    ||   |     |||| |   |    | ||| ||||  | | |  ||    || ||   ||  |||||  | ||    | |  | || |||  ||| | || ||||||||||||||||||||||| |||||||||||||||||||| ||||| |||||| |||| ||||| ||||| ||||| |||||||||||||
-----------gttagaatccatgcattg-taatataattatacttaatacttttttcggctttca--aaggaaagcttcttgtc---tacagaatttcataaggtctgcaactgatatggactgagaactgctaatcagaat-gtatcat-atatttcacagGCATTCAATGGTAAAAAGTGGGAGAAGTTCAACAGTGAGAAGGTGGCATCTCTTGCATATGCTCGAATTCAAGGAAAAACTGCTCTTATTGCTCATTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: Vv00s0239g00110.t01 (Vitis vinifera), 3'ss of exon 3
gtcagaaaattattccaattgacgaagtgctactgcattg-atgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
            ||  |||  | | | ||  |    |||  |  |||  || |   | |   |      ||    | |    | |  |||||   | |       | | | |   || ||   ||  |||||  | ||    | |  | || |||  ||| | || ||||| ||||||||||||||||| || ||||||||||||||||| ||||| ||||||  |||  |||| ||||| ||||| | |||||||||||
-----------gtttgaatccatggattgtaatataattatacttaatatttttttcgactttcaaaggaaagcttcttgtctacagaattt---cataaggtctacaactgatatggactgagaactgctaatcagaat-gtatcat-atatttcacagGCATTCAATGGAAAAAAGTGGGAGAAGTTCAATAGTGAGAAGGTGGCATCTCTTGCATATGCTCAAATTTAAGGAAAAACTGCTCTTACTGCTCATTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: EFJ28199 (Selaginella moellendorffii), 3'ss of exon 12
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcc-tgagccattttgtcatc--tttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                                                                                                               | |||| || ||  ||  | | | || ||  | |  |  ||  | || ||||| || ||||| || |||||||||||||| ||||| |||||||| || || || ||||| ||| |||| ||||| ||    || ||  | || |||||||
---------------------------------------------------------------------------------------------------------------gtttga-caccgttgttttcttcgtgcgcattctcattctcgatcttacagACCTTCAATGGAAAGAAGTGGGAGAAGTTCAACAGCGAGAAGGTTGCTTCTCTGGCTTACGCTCGAATACAAGGCAAGGTTGCCCTCGTCGCACATTTCC

upper sequence: GRMZM2G459746_T01 (Zea mays), 3'ss of exon 13
lower sequence: EFJ16044 (Selaginella moellendorffii), 3'ss of exon 8
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatcttttt---cagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                                                                                        | | |      |  | | |   |  ||    | |||| ||   | || |  | | |  |  | | |||   ||||| || ||||| || || ||||||||||||||||| |||||||||||||| || || || ||  | |||||||| ||  | || ||||| || || ||||
--------------------------------------------------------------------------------------gttctctgtgaaaaagagagaggagattttccta-cgacttg--gttctaaaacttgtcattctttgttttcacagACGTTCAATGGCAAGAAATGGGAGAAGTTTAACAGCGAGAAGGTGGCATCGCTCGCGTACGCGCGGATCCAAGGCAAGGCCGCGCTGATCGCGCACTTCC

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), 43 (downstream exon)
Score: 71

AATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAGgtcagaaaat ... tctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 65

AATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAGgtcagaaaat ... tctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC


Block sizes: 49 (upstream exon), 43 (downstream exon)
Score: 43

AATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAGgtcagaaaat ... tctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC


Block sizes: 48 (upstream exon), 43 (downstream exon)
Score: 46

AATAAATGTAATGTTGGCTATGCTTTCATCAACATGACCAATGCTCAGCATATCATTCCATTTTATCAGgtcagaaaat ... tctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC
                                     ttttgtcatctttttc  CT-rich tract
                                            atcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcagaaaattattccaattgacgaagtgctactgcattgatgtaaagttgtaaactagcctttggtcaacttatatgccttgccaaatttgtactttgataaaatatccggcttgaacatcgacgtgctatcctgagccattttgtcatctttttcagACTTTTAATGGTAAAAAGTGGGAGAAGTTTAACAGTGAGAAGGTGGCATCACTTGCTTATGCTAGAATCCAAGGGAAAACAGCTCTGATTGCTCATTTCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC