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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagtatcaggattacttattctaataaatgaatacttctctattaaggtaaaggggctaatctgttctgtgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG

Basic information

species Zea mays
transcript GRMZM2G101250_T01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101250_T01 (Zea mays), 3'ss of exon 15
lower sequence: LOC_Os04g09860.3 (Oryza sativa), 3'ss of exon 16
gtaaagtatcagg-attacttattctaataaatgaatacttctctattaaggtaaag-gggctaatctgttctgtg-cctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
|||||||| ||||  |   ||     ||||  | || |||  |   | || ||||   | |   |    || |||| | ||||||||||||||| ||||||| ||||| |||||||||| ||| || || |||||
gtaaagtaccaggcgtctttttagtcaatacttcaacactgttaattcaaagtaagttgagaggagtgcttatgtggcttttcagGTTGGTGGTACAGCTTCAACAGCAGGCCTTGCACCAGTTCTAGAACAAAG
















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|60399530|gb|DN232341.1|DN232341
EST:     GGACGTGTTGCCCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTGGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GGACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|60358881|gb|DN225854.1|DN225854
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|148934268|gb|EC878291.2|EC878291
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|78121627|gb|DV540011.1|DV540011
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|40302924|gb|CK347311.1|CK347311
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|60358880|gb|DN225853.1|DN225853
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|32834623|gb|CD974301.1|CD974301
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|32930313|gb|CF035125.1|CF035125
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|32833197|gb|CD972875.1|CD972875
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
EST: gi|91056340|gb|EB166758.1|EB166758
EST:     GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTG                         GTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
genomic: GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG

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: 48 (upstream exon), 47 (downstream exon)
Score: 249

GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG


Block sizes: 49 (upstream exon), 47 (downstream exon)
Score: 95

GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG


Block sizes: 46 (upstream exon), 47 (downstream exon)
Score: 84

GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG


Block sizes: 48 (upstream exon), 47 (downstream exon)
Score: 171

GACGTGTTGACCTTCAAAAGAAGCTGTTTGGTAGCATTCAGTTGgtaaagtatc ... tgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaatgaatacttctctattaaggtaaaggggctaatctgttctgtgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG
                              ggctaat  putative branch site (score: 171)
                                             tgcctttc  putative PPT
              tctattaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagtatcaggattacttattctaataaatgaatacttctctattaaggtaaaggggctaatctgttctgtgcctttcagGTTGGTGGTGCAGCTTCTACAGCTGGCCTTGCACAAGTGCTGGAGCAAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG