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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagcttgtggaacaccaaagatttccatccctaatacgactctctgctgcttgtatgagatcatttatgactcggtgcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g35400.4 (Oryza sativa), 3'ss of exon 7
gttagct-tgtggaacaccaaagatttccatccctaatacgactctctgctgcttgtatgagatcatttatgac-tcggtgcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG
||||| | | |||| |     |     | |||   |  | | || | ||  | ||     |  |||||| |  | |  |||||  |||||| || |||||||| |||||| |  |||| ||  |||||   ||||||||    || || || || ||||||||||||||||| ||||||||||||
gttagttatctggaccctggcacggacctatc---aggatgcctatatgtagttttatataattcatttctttcatttgtgcaatttcagCAATAGTTAGTTTTGGAGATGTGACAAGTGAACTGAAAAGAGAAGCTGAACAGTTAGGAGTATCTTGCTTTTCTTGGGAAGAATTTTCTTCAATG
















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|148958443|gb|EC904677.2|EC904677
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|148995832|gb|EE035067.2|EE035067
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|211174084|gb|FL129199.1|FL129199
EST:     ATACTAGCAGNTCTCCCTAAGNGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|211345429|gb|FL132812.1|FL132812
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|149076511|gb|EE165137.2|EE165137
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|87157287|gb|DY402076.1|DY402076
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|211174085|gb|FL129200.1|FL129200
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGANA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|149086279|gb|EE175820.2|EE175820
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|149107582|gb|EE189463.2|EE189463
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|71430909|gb|DR811959.1|DR811959
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|149073920|gb|EE162247.2|EE162247
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|149098382|gb|EE184358.2|EE184358
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTG
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTG
EST: gi|211174083|gb|FL129198.1|FL129198
EST:     ATACTAGCAGTTCTCCCCTAAGTGCACAGCGCACCTTANAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGGGAGATGAAA
genomic: ATACTAGCAGTTCTCCC-TAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAA
EST: gi|148942583|gb|EC887602.2|EC887602
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|93282461|gb|EB674725.1|EB674725
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|149085816|gb|EE175338.2|EE175338
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|148970227|gb|EE021164.2|EE021164
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|211174082|gb|FL129197.1|FL129197
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|211174078|gb|FL129193.1|FL129193
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|211175750|gb|FL129201.1|FL129201
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|148999540|gb|EE036511.2|EE036511
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|211399266|gb|FL448654.1|FL448654
EST:     ATAGTAGCAGTTCTCCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCT-CCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
EST: gi|211175754|gb|FL129205.1|FL129205
EST:     ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAG                         CCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA
genomic: ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGA

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 3 RNA-Seq libraries.


Block sizes: 45 (upstream exon), 49 (downstream exon)
Score: 274

ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 174

ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG


Block sizes: 40 (upstream exon), 49 (downstream exon)
Score: 514

ATACTAGCAGTTCTCCCTAAGTGCACAGCGCACCTTAGAGgttagcttgt ... gcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatacgactctctgctgcttgtatgagatcatttatgactcggtgcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG
 ccctaat  putative branch site (score: 514)
                            atcatttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagcttgtggaacaccaaagatttccatccctaatacgactctctgctgcttgtatgagatcatttatgactcggtgcatgttcagCCATTGTTAGTTTCGGAGATTTTGCAAGCGAGATGAAAGCGGAAGCTGAGAGATTGGGCGTCTCCTGCTTTTCTTGGGAAGAGTTTTCTTCAATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA