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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctattagttagattccaattcctcaaaatgtagacgttttcataagtgtgattgttatatggtaacgagttaataacttgcactgtttctctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTTTGGTTAGGAAGATCGTGCATGTGCTCAAGAGAGCATCGCTTATTGTCTT

Basic information

species Zea mays
transcript GRMZM2G149576_T01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G149576_T01 (Zea mays), 3'ss of exon 10
lower sequence: LOC_Os03g51650.1 (Oryza sativa), 3'ss of exon 10
ctattagttagattccaattcctcaaaatgtagacgttttcataagtgtgattgttatatggtaacgagt---taataacttgcactgtttctctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTTTGGTTAGGAAGATCGTGCATGTGCTCAAGAGAGCATCGCTTATTGTCTT
                |||||||    |||   |  | |   ||    |     ||  |  |||||   |   |||| |  || ||||||| |    ||||||||| |||| | |||| ||||||||||||||||||||||||||||||||  |||||  ||||  ||||||| ||||||||| ||||||| || ||||||||
--------------gtaattcct--ggatgctaatatctgtttagaaatagcatttccaaagtaaccgttcaataatgatgtgaactgtttgttc--ctgcagCTGTCTACTTGATCTGCATTTCCATATTGGCTGGATTCTGGGGCCAGTCCTTGGTCCGGAAACTCGTGCACGTGCTCAAGCGAGCATCTCTGATTGTCTT
















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|12047343|gb|BF729482.1|BF729482
EST:     CTCTCTGTGGTGGAGTTCTANCTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CTCTCTGTGGTGGAGTTTTA-CTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|76917338|gb|DV166773.1|DV166773
EST:     CCTTTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGGTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|71772905|gb|DR970828.1|DR970828
EST:     GTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: GTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|76013548|gb|DT940718.1|DT940718
EST:     CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|78111898|gb|DV530295.1|DV530295
EST:     CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|78088724|gb|DV517117.1|DV517117
EST:     CACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|13198414|gb|BG354309.1|BG354309
EST:     CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|13316011|gb|BG410458.1|BG410458
EST:     CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAG-GTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|94472463|gb|EB701421.1|EB701421
EST:     TTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: TTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|44900512|gb|CK827057.1|CK827057
EST:     AGTTTTATTTCCTGCACAGTTTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTTCCATATTGGCTGGATTCTGGGGCCAGTGT
genomic: AGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCA-TTTCCATATTGGCTGGATTCTGGGGCCAGTGT
EST: gi|211390817|gb|FL199661.1|FL199661
EST:     TCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: TCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|33099896|gb|CF059856.1|CF059856
EST:     CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|71429318|gb|DR810368.1|DR810368
EST:     CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|33099796|gb|CF059756.1|CF059756
EST:     CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|91877727|gb|EB407684.1|EB407684
EST:     TGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: TGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|116820526|gb|EC863749.1|EC863749
EST:     CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|93282424|gb|EB674688.1|EB674688
EST:     AGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: AGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|91052630|gb|EB163048.1|EB163048
EST:     ACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: ACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|71769067|gb|DR967004.1|DR967004
EST:     TCTGGGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: TCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
EST: gi|78179154|gb|DV549527.1|DV549527
EST:     CCTCTCTGTGGTGGAGTTCTACTTCCTGCACAGATTCCCCCTGCCTTTTG                         CTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT
genomic: CCTCTCTGTGGTGGAGTTTTACTTCCTGCACAGATTCCCCCTGCCTTTTGgtaaatccat ... ctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtgattgttatatggtaacgagttaataacttgcactgtttctctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTTTGGTTAGGAAGATCGTGCATGTGCTCAAGAGAGCATCGCTTATTGTCTT
                         taataac  putative branch site (score: 1)
                                     ctgtttctctatct  putative PPT
     attgttatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctattagttagattccaattcctcaaaatgtagacgttttcataagtgtgattgttatatggtaacgagttaataacttgcactgtttctctatctgcagCTGGCTACCTCATCTTCATTTCCATATTGGCTGGATTCTGGGGCCAGTGTTTGGTTAGGAAGATCGTGCATGTGCTCAAGAGAGCATCGCTTATTGTCTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - tgtgatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acttgca