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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatctggaaagcatatgcatgtgcttatacacacacaaaaaaattttagactatacccaaataatcctttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT

Basic information

species Zea mays
transcript GRMZM2G341404_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os01g74580.2 (Oryza sativa), 3'ss of exon 4
----------------------------------------gtaatctg-gaaagcatatgcatgtgc--ttatacacacacaaaaaaattttagac-tatacccaa-----ataatcctttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT
                                         |  | || |   ||| |  ||  |||  |  || | | |      |  |||| |  | |   ||      | |||  |  ||||||||||||||||||||||| |||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||||||| |||||||||| ||||||
gtaaagcgtatctggtattttaggtttggacaagtgcatgcttgtttgtgcctgcacacacaaatgcagtactagataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTCTGAAGAAGACTAAGAGT

upper sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os02g10180.2 (Oryza sativa), 3'ss of exon 5
----------------------------------------gtaatctg-gaaagcatatgcatgtgc--ttatacacacacaaaaaaattttagac-tatacccaa-----ataatcctttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT
                                         |  | || |   ||| |  ||  |||  |  || | | |      |  |||| |  | |   ||      | |||  |  ||||||||||||||||||||||| |||||||| || || || ||||| ||| |||||||||||||||| ||||| ||||||||| |||||||||| ||||||
gtaaagcgtgtctggtattttaggtttggacaagtgcatgcttgtttgtgcctgcacacacaaatgcagtactagataaatgtgctagctttaaatatttgtacagtgatgacaatattaattgtttagGCACTACCAGAAAGGCCTTCGTCTAGACCCTGAACATTCAGAACTGAAGAAAGCATATTTTGGGTTGAAAAATCTTGTGAAGAAGACTAAGAGT

upper sequence: GRMZM2G341404_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT5G03160.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaatctgga--aagcatatgcatgtgcttatacacacacaaa--aaaattttagac---tatacccaaataatcctttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT
    | |||   ||    |  | | |  | |  || | | |        |   | ||   |||||  || ||| | || |  || ||||| ||||| |||||||||||||||||||| || ||    ||| ||||||||||||| ||||| || ||||| ||  | ||||| || || || 
---gtttggtctaacttcaaccttattttcaatcagagagagtttggggtccaaaacagatatacttaagtaaactttctgtttcagGCATTACCAAAAAGGGCTTCGTCTTGATCCGGAACACAGTGAACTGAAGAAAGCATACTTCGGATTGAAAAAACTGCTCAAGAAAACAAAAAGC

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|148940996|gb|EC885847.2|EC885847
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|149079408|gb|EE168385.2|EE168385
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|148970832|gb|EE021601.2|EE021601
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|78080724|gb|DV509136.1|DV509136
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|71323581|gb|DR798459.1|DR798459
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCTAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|78104565|gb|DV522983.1|DV522983
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|211247228|gb|FL156668.1|FL156668
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAAGGGCTTCGTCT
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAA-GGGCTTCGTCT
EST: gi|91875154|gb|EB405111.1|EB405111
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTC
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTC
EST: gi|149010182|gb|EE041997.2|EE041997
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|148960799|gb|EE011462.2|EE011462
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|67016841|gb|CO445590.1|CO445590
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
EST: gi|148940390|gb|EC885183.2|EC885183
EST:     TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAG                         GCACTACCAGAGAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA
genomic: TTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAA

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: 136

AGACCGGATTCATTCTAAAGGAAGATGAAGACAACTTGGATGCACTGCTATTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 115

AGACCGGATTCATTCTAAAGGAAGATGAAGACAACTTGGATGCACTGCTATTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 135

AGACCGGATTCATTCTAAAGGAAGATGAAGACAACTTGGATGCACTGCTATTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 301

AGACCGGATTCATTCTAAAGGAAGATGAAGACAACTTGGATGCACTGCTATTACGTGGTCGTGCCTACTATTACCTTGCTGATCATGATGTGGCCTCCAGgtaatctgga ... ttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttatacacacacaaaaaaattttagactatacccaaataatcctttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT
                                         tcctttttgttt  CT-rich tract
           acaaaaaaattttaga  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatctggaaagcatatgcatgtgcttatacacacacaaaaaaattttagactatacccaaataatcctttttgtttagGCACTACCAGAAAGGGCTTCGTCTTGATCCAGAGCATTCCGAATTGAAGAAAGCATATTTCGGGTTAAAAAATCTTTTGAAGAAGACCAAGAGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG