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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagaaaaatcaaacctgaattttgatagaatgtgctaaaaatttacctcgaattgtatgatgatagttttgtttttctatgaaaccatctgattttcttgtcatttatgcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG

Basic information

species Zea mays
transcript GRMZM2G331032_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os02g46510.1 (Oryza sativa), 3'ss of exon 4
gttagaaaaatcaaac-ctgaattttgatagaatgtgctaaaaatttacctcgaattgtatgatgatagttttgtttttctatgaaaccatctga-----ttttcttgtcatttatgcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
|| ||||||||   ||  |||| |  ||||  |   | |||||| | || || ||| || || || |  |||   |||| | ||||| |||||||     |||| || |  | | |||||| | |||| ||||| ||||||||||| ||||| |||||  ||||| ||||| ||||||||||||||||||||||| ||| ||||||||||||| |||
gtgagaaaaatgtgacattgaaataagata--accggataaaaagtcacatcaaatagtttgttgctcattta--ttttgtgtgaaagcatctgaatcattttttttttgttctctgcactgatagCCTTCAGATAAGCCTGTTCCGAATGCCACTCTA-CAAGTTACTGGTGCTGTTGGTTGGAGAAGAGAGGGTCTTATGTACAAGAAGAACGAG

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 4
lower sequence: AT5G46630.1 (Arabidopsis thaliana), 3'ss of exon 4
--------------------gttagaaaaatcaaacctg-aattttgatagaatgtgct------------aaaaatttacctcgaattgtatgatgatagttttgtttttctatgaaac-catctgattttcttgtcatttatgcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                    ||    | ||   |   || |||| || | |  |||| |            |  | | |  | || | |  ||   |||  | ||| || |  |  | |    | ||  ||  |   | | | | || ||||||||   ||| || |||||||||||||| ||  || ||||| || || ||||||||||||||||||||||| ||||  ||||| |||||||||
gtaaaggcatctatttgtttgtgtatacaacagattttgtaattgtgttggtgtgtggttcttcgaagttaagcagtatttcccgcaataaatagagattatgttgcttcttcactagatatgtttgcattcataagcttcttttca-ttacagCCAAAAGACAAACCTGTTCCAAATGCAACA-TTACAAGTTACAGGTGCTGTTGGTTGGAGAAGAGAGGGCCTTGCTTACAAAAAGAATGAG

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 4
lower sequence: Vv02s0012g00910.t01 (Vitis vinifera), 3'ss of exon 4
---------------------------------------------------------------------------gttagaaaaatcaaacctgaattttgatagaatgtgctaaaaatttacctcgaattgtatgatgatagttttgttttt-------ctatgaaaccatctgattttcttgtcatttatgcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                                                                           |||  |   |       |  ||||| |    |  |  | |||||  |  |    || ||| |   |   ||| || ||       |  | | || || |   |||  |||     |   |   | |||| ||||| || || || || ||||| ||| || ||||| || || |||||||||||||| |||||||| ||||| || || |||||||||
gttagatgtttattttagctatacattttggaatctagtaatttgagcagatgaggcattaccgtggatttctaagttgtacttaatgg-tttatattttaagtatacattattaaaatgaagattcctttatattaaagtgaattttttattgaagattccttaatactatttttctttaatgt-gccaaaatataaatagCCTTCAGATAAACCAGTCCCCAATGCAACT-TTACAAGTTACAGGTGCTGTTGGTTGGAGGAGAGAGGGCCTTGTTTATAAAAAGAATGAG

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ22278 (Selaginella moellendorffii), 3'ss of exon 4
gttagaaaaatcaaacctgaattttgatagaatgtgctaaaaatttacctcgaattgtatgatgatagttttgtttttctatgaaaccatctgattttcttgtcatttatgcacttacagCCCTCAGA---GAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                                                                 |||   ||| || |  ||   |   ||| ||  |     ||||||    || ||||||  |||    |  ||     ||||||| |||||  |||||||| || || || || |||||||||||||| ||||| |||||||| ||||||
----------------------------------------------------------------gtagcgatgtgttgcattgc--ctggctggttaac--agaatttatctctttccagCCCATAGATACAAGACCCCCAGCAAATGCTACTCTC-CAAGTCACCGGTGCAGTGGGATGGAGAAGAGAGGGTCTTGTTTACAAGAAAAATGAG

upper sequence: GRMZM2G331032_T01 (Zea mays), 3'ss of exon 4
lower sequence: EFJ25669 (Selaginella moellendorffii), 3'ss of exon 4
gttagaaaaatcaaacctgaattttgatagaatgtgctaaaaatttacctcgaattgtatgatgatagttttgtttttctatgaaaccatctgattttcttgtcatttatgcacttacagCCCTCAGA---GAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                                                                 |||   ||| || |  ||   |   ||| ||  |     ||||||    || ||||||  |||    |  ||     ||||||| |||||| |||||||| || || || || |||||||||||||| ||||| |||||||| || |||
----------------------------------------------------------------gtagcgatgtgttgcattgc--ctggctggttaac--agaatttatctttttccagCCCATAGATACAAGACCCCCAGCAAATGCTACTCTT-CAAGTCACCGGTGCAGTGGGATGGAGAAGAGAGGGTCTTGTTTACAAGAAAAACGAG

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|149083894|gb|EE173269.2|EE173269
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|149067461|gb|EE157669.2|EE157669
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCC
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCC
EST: gi|149078564|gb|EE167348.2|EE167348
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|31354959|gb|CD439316.1|CD439316
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCATATGCGACTC-TTCAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|5525788|gb|AI861681.1|AI861681
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTC-TTCAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|91054998|gb|EB165416.1|EB165416
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTC-TTCAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|149090427|gb|EE179737.2|EE179737
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|76918953|gb|DV167527.1|DV167527
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|71445146|gb|DR826196.1|DR826196
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|71304030|gb|DR788136.1|DR788136
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|211055145|gb|FL320202.1|FL320202
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|14202339|gb|BG836016.1|BG836016
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCSTCAGAGAAGCCTGTYC-AAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|76937034|gb|DV175018.1|DV175018
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT
EST: gi|76282279|gb|DV021847.1|DV021847
EST:     TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAG                         CCCTCAGAGAAGCCTGTTCCAAATGCGACTCTT-CAAGTCACTGGCGCTGT
genomic: TGAAGTTGTATATAACTCAAGAAGGTGTTCGGTCACCATTTTCCTCAAAGgttagaaaaa ... gcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagttttgtttttctatgaaaccatctgattttcttgtcatttatgcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG
                       atctgat  putative branch site (score: 4)
        tttttctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagaaaaatcaaacctgaattttgatagaatgtgctaaaaatttacctcgaattgtatgatgatagttttgtttttctatgaaaccatctgattttcttgtcatttatgcacttacagCCCTCAGAGAAGCCTGTTCCAAATGCGACTCTTTCAAGTCACTGGCGCTGTTGGTTGGAGAAGAGAGGGACTTGTGTACAAGAAGAATGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG