Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaatttataagctattttcacctgacactggtaggaccattttgtaaggtatttctcactaccaattaatcgatgacaactctgttctattccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT

Basic information

species Zea mays
transcript GRMZM2G040030_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040030_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os03g55850.1 (Oryza sativa), 3'ss of exon 1
gaatttataagctattttcacctgacactggtaggaccattttgtaaggtat--ttctcactaccaattaatcga-tga--caactctgttctattccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT
     || |    |  |      |   ||  ||        |  | || | |  ||    |     | || | || |||  |  ||||||||| ||| ||| |||||| ||| ||||||||||| | ||||| |||||||||||||||||||| ||||||||||| |||||||||||||| || ||||||  || |||||| |||
-----tacatttaacctgagaacggtccttataaatgtcactcatcagttgtcatttgtgcatttgagtatttgactgaaccccctctgttctcttctactgcagGTACCTCCTGATATTGGATAGGACAAACTGGAAGACCAACATGCTGACCGCTCTCTTGGTCCCTTACATTTTCTTTACACTGCCTGGTGGGCTGTTCTCT

upper sequence: GRMZM2G040030_T01 (Zea mays), 3'ss of exon 1
lower sequence: Vv00s0207g00220.t01 (Vitis vinifera), 3'ss of exon 1
gaatttataagctattttcacctgacactggtaggaccattttgtaaggtatttctcactaccaattaatcga-tgacaactctgttctat-tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT
  |  |||    |  |  |     |  |||          | |  | |  |  |  ||     | || ||  | | |||| | | ||  || |  ||| ||| ||| | |||||| ||||||| ||||| ||||  ||||||||||||||  | || |||||||||||||||||||| |  || |||  |||  ||||    
--agctatggtttgatccctgtgcatcctgaagcatattatgttcacgccaacttgcaggtgaagtttataaactaacaaatattttacatgtttactgcagTTATTTGTTGATACTGGATCGGACAAACTGGAGAACCAACATGCTGACTTCGCTTTTGGTTCCTTACATTTTCTTTAGTCTTCCTCCTGTATTGTTCAAC
















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|211025292|gb|FL190145.1|FL190145
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACCAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|71332001|gb|DR802895.1|DR802895
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|71448580|gb|DR829630.1|DR829630
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|211027745|gb|FL190156.1|FL190156
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACCAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|93012048|gb|EB637568.1|EB637568
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|110204646|gb|EC886543.1|EC886543
EST:     CAAAGGGCTGGCCTTCCTCGCCGCAGT                         GTTTCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|71762702|gb|DR960639.1|DR960639
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|50328812|gb|CO523938.1|CO523938
EST:     CACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|21331512|gb|BQ486893.1|BQ486893
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|76020028|gb|DT947198.1|DT947198
EST:     CCTTCCTCGCCGCAGT                         GTATCTCTGGATATGGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|78116265|gb|DV534652.1|DV534652
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|13149827|gb|BG320149.1|BG320149
EST:     CCTCAAATGGCTGSCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|19822212|gb|BQ048236.1|BQ048236
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|148964237|gb|EE015419.2|EE015419
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|60400506|gb|DN233313.1|DN233313
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACCAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|76010700|gb|DT937870.1|DT937870
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|148972170|gb|EE023041.2|EE023041
EST:     AATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATGGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: AATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|148941605|gb|EC886544.2|EC886544
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|91053646|gb|EB164064.1|EB164064
EST:     CCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|67034400|gb|CO462950.1|CO462950
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|76011638|gb|DT938808.1|DT938808
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|76018464|gb|DT945634.1|DT945634
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACCAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|20336921|gb|BQ172551.1|BQ172551
EST:     TTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCTCAAATTGGAAGACCAACATGCTGACAGC
genomic: TTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|148971030|gb|EE021866.2|EE021866
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|149097933|gb|EE183874.2|EE183874
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|76010827|gb|DT937997.1|DT937997
EST:     TTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: TTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|9254931|gb|BE345399.1|BE345399
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|20208279|gb|BQ134368.1|BQ134368
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|76934209|gb|DV173767.1|DV173767
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|148972171|gb|EE023042.2|EE023042
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
EST: gi|211025293|gb|FL190146.1|FL190146
EST:     CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGT                         GTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC
genomic: CTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGC

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: 387

GCGTCGCCGCGCGGAAGCTCGCCAACCACGCATTCGTCCTCGGCGGCGGGCTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 991

GCGTCGCCGCGCGGAAGCTCGCCAACCACGCATTCGTCCTCGGCGGCGGGCTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 876

GCGTCGCCGCGCGGAAGCTCGCCAACCACGCATTCGTCCTCGGCGGCGGGCTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 682

GCGTCGCCGCGCGGAAGCTCGCCAACCACGCATTCGTCCTCGGCGGCGGGCTGGGGTTCGGCACCTCCTTCCTCAAATGGCTGGCCTTCCTCGCCGCAGTgtgagtgttt ... tccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaggtatttctcactaccaattaatcgatgacaactctgttctattccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT
                                  ctctgttctattcc  CT-rich tract
                  aattaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaatttataagctattttcacctgacactggtaggaccattttgtaaggtatttctcactaccaattaatcgatgacaactctgttctattccactacagGTATCTCTTGATATTGGATCGCACAAATTGGAAGACCAACATGCTGACAGCTCTCTTGGTTCCTTACATTTTCTTCACCCTGCCTAATGTGCTGTTTTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - cacctga