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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttggtgccatgttaggtttcaaatctaacccgcttcaatttgcttgggcctacaaggctttgttgttgctgttggttttctgactaggtttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG

Basic information

species Zea mays
transcript GRMZM2G540403_T03
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G540403_T02 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g15860.1 (Oryza sativa), 3'ss of exon 6
---gttggtgccatgttaggtttcaaatctaacccgcttcaatttgcttgggcctacaaggctttgttgttgctgttggttttctgactaggtttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG
        || | |  || ||     || ||  |    |  |  ||||   |  |   || |||||||   |   | ||||   |||||  ||||  || ||| ||||||| || ||||||||| ||||| || | |||||||||||||| ||| |||| |||||||| |||
gtaaaacttgtcctcctaagtacttcatatagtcaatatgcaagtgctaatgattc--agactttgtttggggcat-ggttgattgactccgtttggctgcagATTCAGGACCTTTACAAAGAAGCTGGATTTTTGGGCTTCTGGAAAGGTGTAGTTCCAGCTCTTATTATG
















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|24934302|gb|CA452520.1|CA452520
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|149071944|gb|EE160331.2|EE160331
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGG
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGG
EST: gi|78120502|gb|DV538886.1|DV538886
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|211096941|gb|FL476436.1|FL476436
EST:     GCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: GCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|148952677|gb|EC898511.2|EC898511
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|91877627|gb|EB407584.1|EB407584
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|32929640|gb|CF034452.1|CF034452
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACAATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|71766550|gb|DR964487.1|DR964487
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|76936044|gb|DV174582.1|DV174582
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|149027549|gb|EE046558.2|EE046558
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|71422924|gb|DR805897.1|DR805897
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
EST: gi|71448089|gb|DR829139.1|DR829139
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAG
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAG
EST: gi|211285344|gb|FL118293.1|FL118293
EST:     CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATATAAAACAATTGATGTT                         TTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA
genomic: CCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTA

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), 49 (downstream exon)
Score: 97

GGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 133

GGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG


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

GGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 149

GGCAAACAAACAGCAAAGACCTCAGGGTTTGAATTGTGCTCTTGATAAGCCCCTTGAAGCTGCTACAGCTGAAAACGCTCCATACAAAACGATTGATGTTgtaagtacaa ... ttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggcctacaaggctttgttgttgctgttggttttctgactaggtttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG
                                            tttaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtgccatgttaggtttcaaatctaacccgcttcaatttgcttgggcctacaaggctttgttgttgctgttggttttctgactaggtttaactccagTTTCAGGAACTCTACAAAGAATCTGGAGTTCTTGGCTTCTGGAAAGGGGTAATTCCGGCTCTTATCATG

- tggtgcc
- - - - - - - - - - - - - - - ccgcttc
- - - - - - - - - - - - - - - - - - - - -tgcttgg
- - - - - - - - - - - - - - - - - - - - - - - - gcctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gttgctg