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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgatttactgttttgatcagatcgacccatgaatgaaactttactttcggttgcagcatttccattccccaacttatcttctcaaatggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG

Basic information

species Zea mays
transcript GRMZM2G362088_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os03g05740.1 (Oryza sativa), 3'ss of exon 3
----------------gtgatttactgtt--ttgatcagatcgacccatgaat--gaaactttactttcggttgcagcatttccat--tccccaacttatcttctcaaatggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG
                ||   ||| | |   ||||| |  |    |      |  ||  | | | | |   || ||| | ||| ||  |    ||||||| | |||||||  || ||||||||||| || ||||| |||||||||||||||||||| |||||||| |||||||||||||| |||||||| |||||||| ||||| ||||||||
gtgattactgttttgagtctcttagtttcagttgataatgttattcttcaccttagatgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCAACAATAGTGAAATTTGAAATATGGGATACCGCTGGACAAGAGAG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA20G32320.1 (Glycine max), 3'ss of exon 3
--------------------------------gtgatttactgt---tttgatcagatcgacccatgaatgaaacttta---ctttcggttgcagcatttccat------tccccaacttatcttc--tcaaatggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG
                                 |  |||| | |   |||  | |    |    ||||   ||| |||    ||||   |   |    ||||||      |  |  |  | | ||        |  |   ||||||||||||| || |||||||| ||||||||| | ||  || | || || |||| ||| ||||||||||| |||||||||||||| ||||||||
gtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgttaattattccatggaaattttcttatatgttttagactctgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCACAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG

upper sequence: GRMZM2G362088_T02 (Zea mays), 3'ss of exon 4
lower sequence: GLYMA10G35230.3 (Glycine max), 3'ss of exon 3
-------------------------------------gtgattta--ctgttttgatcagatcgacccatgaatgaaactttactttcggt-tgc-agcatttccat----tccccaacttatcttctcaa----atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG
                                      | || ||   | |||| ||    |  |      ||  | | | |  | | | | ||  |    ||||||    |        ||| || |  |     |  |   ||||||||||||| || |||||||| || |||||| | ||  || | || || |||| ||| ||||||||||| |||||||||||||| ||||||||
gtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaattattccatggaattgttcttatatgttttagactttgtaatgtaagGTAACTGTTGGAGCTTCTTTTTTGTCGCAAACAATAGCTCTGCAAGACTCTACAACAGTCAAGTTTGAAATATGGGATACTGCTGGTCAAGAGAG

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|211329193|gb|FL235162.1|FL235162
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGTTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331361|gb|FL235186.1|FL235186
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGGAGGATTC
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGG-AGGATTC
EST: gi|211329196|gb|FL235165.1|FL235165
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331350|gb|FL235175.1|FL235175
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCCTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211329203|gb|FL235172.1|FL235172
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331353|gb|FL235178.1|FL235178
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|50330001|gb|CO525127.1|CO525127
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211329194|gb|FL235163.1|FL235163
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCCTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|148937431|gb|EC881612.2|EC881612
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331363|gb|FL235188.1|FL235188
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|5525847|gb|AI861740.1|AI861740
EST:     GTTGCATTGTTCTTCGTTTTGTTCGGGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGATGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331355|gb|FL235180.1|FL235180
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|60336834|gb|DN203807.1|DN203807
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331359|gb|FL235184.1|FL235184
EST:     GTTGCATTGTTCTTCGBTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331360|gb|FL235185.1|FL235185
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCCTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331354|gb|FL235179.1|FL235179
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211329201|gb|FL235170.1|FL235170
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCCTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331364|gb|FL235189.1|FL235189
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCCTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211333515|gb|FL235190.1|FL235190
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|78089132|gb|DV517518.1|DV517518
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211329204|gb|FL235173.1|FL235173
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCCTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211331358|gb|FL235183.1|FL235183
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCCTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211329197|gb|FL235166.1|FL235166
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCCTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
EST: gi|211329200|gb|FL235169.1|FL235169
EST:     GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAG                         GTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA
genomic: GTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCA

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: 45 (upstream exon), 46 (downstream exon)
Score: 193

TTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 353

TTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG


Block sizes: 48 (upstream exon), 48 (downstream exon)
Score: 426

TTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 324

TTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttact ... atggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttactttcggttgcagcatttccattccccaacttatcttctcaaatggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG
                              aacttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgatttactgttttgatcagatcgacccatgaatgaaactttactttcggttgcagcatttccattccccaacttatcttctcaaatggttacagGTAACTGTTGGCGCATCTTTTTTATCACAAACATTGGCATTGGAGGATTCAACAATAGTGAAGTTTGAAATTTGGGATACTGCTGGGCAAGAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA