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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag

Basic information

species Zea mays
transcript GRMZM2G408989_T01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G408989_T03 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os05g45310.1 (Oryza sativa), 5'ss of exon 5
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag
||||| ||||||||||||| ||||||||||| ||||| |||||||| ||||| ||||||||||||| ||||| ||||  |||| |||  |||| |                |  ||||  |||       ||| ||||| |||||||||| |   |||||
CTTGGATTGCTGGTTTGGTCCAAACAGCTCTTTATGCGGATTTCTTCTACTACTATTTCTTAAGgtaaactggatactgttgtcaaacctcatttg---------------cagactctctgg-------gtactgacaattccatgtcggttgttgcag

upper sequence: GRMZM2G408989_T03 (Zea mays), 5'ss of exon 4
lower sequence: GLYMA08G12570.1 (Glycine max), 5'ss of exon 5
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag
| ||     | ||| | || || |||||| |||||||||||||||| |||||||||||| | |||| |  |   |  |  ||| ||     || |  ||    | |||  || ||   |     |    | |||    | ||   | | |          
CCTGTGCCTCAGGTGTTGTTCAGACAGCTTTGTATGCAGATTTCTTCTACTATTATTTCATCAGgtaatgttattgtc--tgttaaggtcgatcttgtttttgt-tatgctcatataac--aaatgggtaatataaggagttttgttttgcag-------
















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|18169894|gb|BM339734.1|BM339734
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|16920990|gb|BM074929.1|BM074929
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|91871430|gb|EB401416.1|EB401416
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATG
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATG
EST: gi|91871428|gb|EB401415.1|EB401415
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|78023775|gb|DV492162.1|DV492162
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|78023788|gb|DV492175.1|DV492175
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|50330722|gb|CO525848.1|CO525848
EST:     GGTGNCAA-CAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTNNAG                         T-GGAAGAACNACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTT
genomic: GGTG-CAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTA-AGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTT
EST: gi|16922820|gb|BM075812.1|BM075812
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|6022165|gb|AW067093.1|AW067093
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|60344375|gb|DN211348.1|DN211348
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|14245658|gb|BG874240.1|BG874240
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|78080743|gb|DV509155.1|DV509155
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|211107178|gb|FL251311.1|FL251311
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAACATGCTTCGTCAT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|24769505|gb|CA404634.1|CA404634
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|31354771|gb|CD439128.1|CD439128
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|60342889|gb|DN209862.1|DN209862
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|18169973|gb|BM339813.1|BM339813
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|18165355|gb|BM335194.1|BM335194
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
EST: gi|78080744|gb|DV509156.1|DV509156
EST:     TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAG                         TTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT
genomic: TTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGT

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), 47 (downstream exon)
Score: 168

CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGTGCCAGAAAGTGTGCATGCTACATGACTCAAGTTTTCTAGAAATTTGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 147

CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGTGCCAGAAAGTGTGCATGCTACATGACTCAAGTTTTCTAGAAATTTGTTT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 125

CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGTGCCAGAAAGTGTGCATGCTACATGACTCAAGTTTTCTAGAAATTTGTTT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 190

CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgca ... atcactgcagTTGGAAGAACAACGTGAAGCTCGAGTTGCCTGCTTGAGCATGCTTCGTCGTGCCAGAAAGTGTGCATGCTACATGACTCAAGTTTTCTAGAAATTTGTTT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTTGGCTTGCTGGTTTGGTGCAAACAGCTCTGTATGCAGATTTCTTTTACTATTATTTCTTAAGgtgaactgcataccattgtgaaatgtcatatcattaacatctatcatcgtactccttggttactgagtattgacacttccatgtcgatcactgcag

- - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - -  GCAGAT