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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCCTAAGGACGAATGCGTGGGCGTGACTCCCCCACTCGCTATGAAGCCCAAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacctgcaatctgttcgattttctgccggagtctgttgaggattcagatttacagttctttgttaccctttgcgtgcag

Basic information

species Zea mays
transcript GRMZM2G098714_T01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G098714_T01 (Zea mays), 5'ss of exon 3
lower sequence: LOC_Os03g11540.1 (Oryza sativa), 5'ss of exon 3
AGCCTAAGG--ACGAATGCGTGGGCGTGACTCCCCCACTCGCTATGAAGCCCAAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaag---tacctgcaa-------------tctgttcgatt--ttctgccggagt-ctgttgaggattcagatttacagttctttgttaccctt-tgcgtgcag
   | |||   ||||| |||  | |     ||| ||  | |   ||||||||||||||||||||||||| ||||||||||||||||| |||||||| || |||||||   | | ||| |               |||||  ||  |||||  | ||   |||||  ||  |  |  | | | |  ||| | || |  ||  |||||
TCTCCAAGCCCACGAACGCGCCGCCAC--TTCCTCCGGTTGTGCTGAAGCCCAAGCAGGAGGTGAAGTCCGCGTCCCAGATCGTGAACGAGCAGCGCGGCAAgtaagcgattcttgcgagatccccatctctcttgttcagttgtttctgatgcagaattgttggtgagactaacctgccgattcttgatgccttcctgtttgcag
















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|26455797|gb|CA827380.1|CA827380
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
EST: gi|29945007|gb|CB815421.1|CB815421
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCTTT
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTT
EST: gi|211343901|gb|FL063190.1|FL063190
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCCTTTC-ATGACAAAGAGGGTCCATCCNTTTG
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCC-TTTCCATGACAAAGAGGGTCCATCC-TTTG
EST: gi|19770120|gb|BQ034841.1|BQ034841
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
EST: gi|211343898|gb|FL063187.1|FL063187
EST:     AGCANGAGGGTGA-GTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCTTTC
genomic: AGCAGGAGG-TGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTC
EST: gi|5555566|gb|AI881517.1|AI881517
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGNGAATGAGCAGCGTGGAAA                         TACTGCTCCTG
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTG
EST: gi|211343899|gb|FL063188.1|FL063188
EST:     AGNNAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCA
genomic: AGC-AGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCA
EST: gi|211343902|gb|FL063191.1|FL063191
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCA-GCCCCTTTTCATGACAAAGAGGGTCCCATCCTTTGA
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCC-ATCCTTTGA
EST: gi|211343905|gb|FL063194.1|FL063194
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCTTTC
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTC
EST: gi|29945326|gb|CB815583.1|CB815583
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
EST: gi|71438959|gb|DR820009.1|DR820009
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
EST: gi|5268729|gb|AI770693.1|AI770693
EST:     AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAA                         TACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT
genomic: AAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGAT

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: 47 (upstream exon), 49 (downstream exon)
Score: 191

AGCCTAAGGACGAATGCGTGGGCGTGACTCCCCCACTCGCTATGAAGCCCAAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGATCACTCTGAACCCCTACCAGGGTAACTGGGTCATTAAGGTGCGGGTCACG


Block sizes: 44 (upstream exon), 47 (downstream exon)
Score: 34

AGCCTAAGGACGAATGCGTGGGCGTGACTCCCCCACTCGCTATGAAGCCCAAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGATCACTCTGAACCCCTACCAGGGTAACTGGGTCATTAAGGTGCGGGTCACG


Block sizes: 47 (upstream exon), 48 (downstream exon)
Score: 27

AGCCTAAGGACGAATGCGTGGGCGTGACTCCCCCACTCGCTATGAAGCCCAAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGATCACTCTGAACCCCTACCAGGGTAACTGGGTCATTAAGGTGCGGGTCACG


Block sizes: 34 (upstream exon), 22 (downstream exon)
Score: 12

AGCCTAAGGACGAATGCGTGGGCGTGACTCCCCCACTCGCTATGAAGCCCAAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacct ... ttgcgtgcagTACTGCTCCTGTCAAGCCCCTTTCCATGACAAAGAGGGTCCATCCTTTGATCACTCTGAACCCCTACCAGGGTAACTGGGTCATTAAGGTGCGGGTCACG


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCCTAAGGACGAATGCGTGGGCGTGACTCCCCCACTCGCTATGAAGCCCAAGCAGGAGGTGAAGTCTGCGTCCCAGATCGTGAATGAGCAGCGTGGAAAgtaagtacctgcaatctgttcgattttctgccggagtctgttgaggattcagatttacagttctttgttaccctttgcgtgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG