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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatacattcctaaaatattgtagcctttccttaactaacctgatgaaaaaaggaaattaattccagtattttattgtaatatgcttgttgctaaatattgttttaccag

Basic information

species Zea mays
transcript GRMZM2G094123_T01
intron # 7
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G094123_T01 (Zea mays), 5'ss of exon 7
lower sequence: LOC_Os12g25710.3 (Oryza sativa), 5'ss of exon 7
CAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac---attcctaaaatatt--------gtagcctttccttaactaacctgatgaaaaaaggaaattaattccagtattttattgtaatatgcttgttgctaaatattgttttaccag
| ||||||| || |||||||||||||||||||||||||| |||||||| ||||||||||||||||||||||| ||||| || ||||| || || ||||||||||| |||    ||   |     |||         |||  ||||  ||  || ||||||||| ||  | | |||  |  | |||||  |  |||||   || ||   | || |||         
CCGAAGGATTTATGAAGAATTTTTAGCAGTTCCAGTTTCTAAAGGGAGGAAAAGTGAGATGGAAAAATTTGCTGGTGGACTGTATACAACAAGTGTTGAGgtattaatatgaaatgtttgcttcattccacccgattagtttttctgtagttaccctgatgaagaagagtacttatcttta-tatttagtaataataaaatt-ttatcatat-ttgcag------
















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|7031274|gb|AW461012.1|AW461012
EST:     AAAGCGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|26559243|gb|CA831478.1|CA831478
EST:     TTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: TTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|91052462|gb|EB162880.1|EB162880
EST:     AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|60338824|gb|DN205797.1|DN205797
EST:     AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|22521630|gb|BU080441.1|BU080441
EST:     AAAGCGAGATGGAAAAATTTGCAGG-GGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|60357064|gb|DN224037.1|DN224037
EST:     AAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|31359187|gb|CD443544.1|CD443544
EST:     AAAGCGAGATGGAAAAATTTGCAGGGGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|67020078|gb|CO448827.1|CO448827
EST:     AAAGCGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|32935632|gb|CF040444.1|CF040444
EST:     AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|67027210|gb|CO455959.1|CO455959
EST:     AAAGCGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|51871150|gb|CV126034.1|CV126034
EST:     AAAGCGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|60346669|gb|DN213642.1|DN213642
EST:     AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
EST: gi|87155487|gb|DY400276.1|DY400276
EST:     AAAGCGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAG                         GCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT
genomic: AAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGT

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: 334

CAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGTCTTGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 350

CAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGTCTTGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 289

CAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGTCTTGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGA


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 347

CAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatac ... gttttaccagGCCTTCATTCCAAACACTGGTCGTGGCATACAAGGCGCAACCTCACACTGTCTTGGTCAAAACTTTGCCAAGATGTTTGATATCACTTTTGAGAATGAGA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAAGGATATACGAAGAATTTTTAGCAGTTCCAGTTTCCAAAGGGAGAAAAAGTGAGATGGAAAAATTTGCAGGTGGCCTTTATACCACCAGCGTTGAGgtattgatacattcctaaaatattgtagcctttccttaactaacctgatgaaaaaaggaaattaattccagtattttattgtaatatgcttgttgctaaatattgttttaccag

- - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA