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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaaagccgaaccttcacagatttatttattttcacagagattttgccctggctttcggatgtcaagctcaactgtttttctaatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATGAGGATTGGATCAGCGATCAGAAGCCTGGGCGTAGAGCCG

Basic information

species Zea mays
transcript GRMZM2G104847_T01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G104847_T01 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os11g35400.4 (Oryza sativa), 3'ss of exon 2
--------------------------gtgaaagccgaaccttcacagatttatttattttcacagagatttt------------gccctggctttcggatgtcaagctcaactgtttttctaataca---------cagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATGAGGATTGGATCAGCGATCAGAAGCCTGGGCGTAGAGCCG
                          | |  |  |  |   | |  |||| |  | |||| | | | |  ||            |   ||  |||    ||  | | |  | | |||||  || | |          |||| ||||| |||||||||| ||| || || ||||||| |||||||||||| | |||||||||||| ||||||||| |  | ||  |||||
gtatgtcaaatctgcatatgtgataagaggcattcagattcttagtgattaagatttttttaaaaaaaacttatgattcaatgtgttttgattttattttgagatggtgcatttttttttaaaaaaaaacaattgttaggctggtgactatgtgtggctaacatatgaagaagtgtaccagAAGGTCATTAAGATTGGATCAGCCATCAGAAGCTTACGTGTCAAGCCG
















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|22542184|gb|BU092622.1|BU092622
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|148958443|gb|EC904677.2|EC904677
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|148995832|gb|EE035067.2|EE035067
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211347818|gb|FL132814.1|FL132814
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GTCGGTGAGTATGTGTGGCAAACGT
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGT
EST: gi|211174084|gb|FL129199.1|FL129199
EST:     GTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: GTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211345429|gb|FL132812.1|FL132812
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|149076511|gb|EE165137.2|EE165137
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|87157287|gb|DY402076.1|DY402076
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211174085|gb|FL129200.1|FL129200
EST:     GTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: GTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|149086279|gb|EE175820.2|EE175820
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|149107582|gb|EE189463.2|EE189463
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|71430909|gb|DR811959.1|DR811959
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|149073920|gb|EE162247.2|EE162247
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211345427|gb|FL132810.1|FL132810
EST:     GTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: GTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|149098382|gb|EE184358.2|EE184358
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211174083|gb|FL129198.1|FL129198
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211345428|gb|FL132811.1|FL132811
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAAGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|148942583|gb|EC887602.2|EC887602
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|9254572|gb|BE345040.1|BE345040
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GGCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211175752|gb|FL129203.1|FL129203
EST:     GTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: GTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|26559314|gb|CA831549.1|CA831549
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211174080|gb|FL129195.1|FL129195
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCANAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|93282461|gb|EB674725.1|EB674725
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|149085816|gb|EE175338.2|EE175338
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAAACGTACGAGGAAGTGTGCCAGAAGGTCAT
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGC-AAACGTACGAGGAAGTGTGCCAGAAGGTCAT
EST: gi|148970227|gb|EE021164.2|EE021164
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211174082|gb|FL129197.1|FL129197
EST:     GTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: GTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211174078|gb|FL129193.1|FL129193
EST:     GTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: GTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211175750|gb|FL129201.1|FL129201
EST:     GTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: GTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|148999540|gb|EE036511.2|EE036511
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211347820|gb|FL132816.1|FL132816
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|76283292|gb|DV022860.1|DV022860
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211175751|gb|FL129202.1|FL129202
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAG
EST: gi|211174081|gb|FL129196.1|FL129196
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|211175754|gb|FL129205.1|FL129205
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATG
EST: gi|94479494|gb|EB708452.1|EB708452
EST:     AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAG                         GCCGGAGAGTATGTGTGG
genomic: AGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGG

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: 398

TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATGAGGATTGGATCAGCGATCAGAAGCCTGGGCGTAGAGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 365

TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATGAGGATTGGATCAGCGATCAGAAGCCTGGGCGTAGAGCCG


Block sizes: 16 (upstream exon), 34 (downstream exon)
Score: 1

TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATGAGGATTGGATCAGCGATCAGAAGCCTGGGCGTAGAGCCG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 771

TGGGGCAGTCAAGAAGTACCCCACGAACAGGATGGTCGGGCAGCGTCAGGTTACAGATGGCAAGgtgaaagccg ... taatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATGAGGATTGGATCAGCGATCAGAAGCCTGGGCGTAGAGCCG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagattttgccctggctttcggatgtcaagctcaactgtttttctaatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATGAGGATTGGATCAGCGATCAGAAGCCTGGGCGTAGAGCCG
                                          ttctaat  putative branch site (score: 771)
                                    ctgtttttct  CT-rich tract
                                       tttttctaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaaagccgaaccttcacagatttatttattttcacagagattttgccctggctttcggatgtcaagctcaactgtttttctaatacacagGCCGGTGAGTATGTGTGGCAAACGTACGAGGAAGTGTGCCAGAAGGTCATGAGGATTGGATCAGCGATCAGAAGCCTGGGCGTAGAGCCG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGC