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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttgtaatctaccaacaatatgctaattcactctgtccaaatttttgagcacgcatcattgcctttctgattcacttctttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGCTTTTCTCCCCCACAAGCAGTAGACTCGAAGGAGGTTGCCAAGGAGGAGG

Basic information

species Zea mays
transcript GRMZM2G014902_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G014902_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os08g06110.2 (Oryza sativa), 3'ss of exon 7
gttgtaatctaccaacaatatgctaattcac-tctgtccaaatttttgagcacgcatcattgcctttctgattcacttctttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGCTTTTCTCCCCCACAAGCAGTAGACTCGAAGGAGGTTGCCAAGGAGGAGG
|| ||  ||||||| || |  ||  |||||| | | ||  | |   ||| ||  ||||| ||| ||||| |||||| | | || || ||||||||||||||||| ||||| ||||||||||| |||| |||||| |||||||||||||| || |||| || ||  || |||||| ||  ||||||||| |
gtggtcgtctaccagcattccgcatattcacatttatcttactcgctgaacatccatcactgcttttctaattcacatttctgctgtcagGGTCGTCTGGCTTTTGATGCACTGTTCAGTAGAGAAAGGCTTCCCCAAAGCTTTTCTCCTCCGCAAGTAGAAGGATCAAAGGAGATTAGCAAGGAGGAAG
















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|32850186|gb|CD989867.1|CD989867
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|4646414|gb|AI621739.1|AI621739
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|60343801|gb|DN210774.1|DN210774
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|78104586|gb|DV523004.1|DV523004
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|94473787|gb|EB702745.1|EB702745
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|67018514|gb|CO447263.1|CO447263
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|18168241|gb|BM338087.1|BM338087
EST:     GTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: GTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|33099349|gb|CF059309.1|CF059309
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|60395782|gb|DN228652.1|DN228652
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|26559873|gb|CA832108.1|CA832108
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|60346693|gb|DN213666.1|DN213666
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|60339696|gb|DN206669.1|DN206669
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|211246879|gb|FL472900.1|FL472900
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|71307765|gb|DR790101.1|DR790101
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|78104585|gb|DV523003.1|DV523003
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|60401593|gb|DN234400.1|DN234400
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|60337383|gb|DN204356.1|DN204356
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|22819635|gb|BU499725.1|BU499725
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|71419072|gb|DR804639.1|DR804639
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|83278724|gb|DV942732.1|DV942732
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|13562300|gb|BG550520.1|BG550520
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|33098822|gb|CF058782.1|CF058782
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
EST: gi|87157141|gb|DY401930.1|DY401930
EST:     TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAG                         GGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC
genomic: TTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGC

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: 127

GCAAGCCTCCTGCAGCAACTCTTCAGCTGGTGACACTAACCACCGCAGATTTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGCTTTTCTCCCCCACAAGCAGTAGACTCGAAGGAGGTTGCCAAGGAGGAGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 91

GCAAGCCTCCTGCAGCAACTCTTCAGCTGGTGACACTAACCACCGCAGATTTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGCTTTTCTCCCCCACAAGCAGTAGACTCGAAGGAGGTTGCCAAGGAGGAGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 153

GCAAGCCTCCTGCAGCAACTCTTCAGCTGGTGACACTAACCACCGCAGATTTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGCTTTTCTCCCCCACAAGCAGTAGACTCGAAGGAGGTTGCCAAGGAGGAGG


Block sizes: 46 (upstream exon), 45 (downstream exon)
Score: 62

GCAAGCCTCCTGCAGCAACTCTTCAGCTGGTGACACTAACCACCGCAGATTTAGAAGCAATGGAAGCACAAGTGATTCATGGAAGGAAGTTTCCGAAGAGgttgtaatct ... ttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGCTTTTCTCCCCCACAAGCAGTAGACTCGAAGGAGGTTGCCAAGGAGGAGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtccaaatttttgagcacgcatcattgcctttctgattcacttctttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGCTTTTCTCCCCCACAAGCAGTAGACTCGAAGGAGGTTGCCAAGGAGGAGG
                              ttctgat  putative branch site (score: 62)
                                    ttcacttctttgtt  CT-rich tract
     aatttttga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgtaatctaccaacaatatgctaattcactctgtccaaatttttgagcacgcatcattgcctttctgattcacttctttgttgacagGGTCGTCTGGCTTTCGATGCGCTGTTCAGTAGGGAAAAGCTTCCGCAAAGCTTTTCTCCCCCACAAGCAGTAGACTCGAAGGAGGTTGCCAAGGAGGAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG