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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCAGAGATGGGGCTTAAACTGCGGGTTGACATGCCTCAGCAGGCTATGGATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaagtctactggatccatagttcgtcatcttgtctccattttagtaattttggatatttggattaacagtttatttgtggttattcatacttattag

Basic information

species Zea mays
transcript GRMZM2G140917_T01
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G140917_T01 (Zea mays), 5'ss of exon 11
lower sequence: LOC_Os06g48770.2 (Oryza sativa), 5'ss of exon 10
TTCAGAGATGGGGCTTAAACTGCGGGTTGACATGCCTCAGCAGGCTATGGATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaagtctactggatccatagttcgtcatcttgtctccattttagtaattttggatatttggattaacagtttatttgtggttattcatacttattag
| | |||||||||||||| |||||||||||||||||| ||||||||||||| || || |||||||| ||||| ||||| || ||||||| |||||||||||||||    || ||||     |  || |  || |||    |||  || || |||||| |||  ||||||||||| ||||  || ||  | ||| |         
TGCGGAGATGGGGCTTAAGCTGCGGGTTGACATGCCTGAGCAGGCTATGGAGATCGCTACAGTATTTTTTCGGCAGTCCACTACAGCAAATGAAGCAAAGgtagg----aggctaccactactgtaatctgt-atccctcctc--ttgtattaattt-ggaagtttggattaactgtttggttatgacttttctttag------
















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|211142855|gb|FL032416.1|FL032416
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211402616|gb|FL252144.1|FL252144
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211145716|gb|FL032440.1|FL032440
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144286|gb|FL032428.1|FL032428
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144291|gb|FL032433.1|FL032433
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211145718|gb|FL032442.1|FL032442
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|148966697|gb|EE017760.2|EE017760
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144288|gb|FL032430.1|FL032430
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211145719|gb|FL032443.1|FL032443
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144285|gb|FL032427.1|FL032427
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211142858|gb|FL032419.1|FL032419
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211145714|gb|FL032438.1|FL032438
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211145713|gb|FL032437.1|FL032437
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211145715|gb|FL032439.1|FL032439
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144284|gb|FL032426.1|FL032426
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144294|gb|FL032436.1|FL032436
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144287|gb|FL032429.1|FL032429
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211145717|gb|FL032441.1|FL032441
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144283|gb|FL032425.1|FL032425
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211142856|gb|FL032417.1|FL032417
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144292|gb|FL032434.1|FL032434
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144280|gb|FL032422.1|FL032422
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211142860|gb|FL032421.1|FL032421
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144290|gb|FL032432.1|FL032432
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211142857|gb|FL032418.1|FL032418
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211142859|gb|FL032420.1|FL032420
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
EST: gi|211144282|gb|FL032424.1|FL032424
EST:     ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAG                         GAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT
genomic: ATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTT

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: 38

TTCAGAGATGGGGCTTAAACTGCGGGTTGACATGCCTCAGCAGGCTATGGATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 204

TTCAGAGATGGGGCTTAAACTGCGGGTTGACATGCCTCAGCAGGCTATGGATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 282

TTCAGAGATGGGGCTTAAACTGCGGGTTGACATGCCTCAGCAGGCTATGGATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 211

TTCAGAGATGGGGCTTAAACTGCGGGTTGACATGCCTCAGCAGGCTATGGATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaa ... tacttattagGAGAACATAAAAACACTTAATGACCAAAGAGAGAGAAATGTCAAAGCTCTTCAAGAAAAGATGAAATTGAACAAGAAGGAGGTTCAACGCTTTAATCCT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCAGAGATGGGGCTTAAACTGCGGGTTGACATGCCTCAGCAGGCTATGGATATTGCCACAGTATTCTTTCGTCAGTCAACCACAGCAAGTGAAGCAAAGgtaggctgaagtctactggatccatagttcgtcatcttgtctccattttagtaattttggatatttggattaacagtttatttgtggttattcatacttattag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG