Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttgtgctgccaacccaccatttggacaatgtgaagtttgcttaaatgccaggtgccttttgcttaaacgcttaggctatatgctgattcttattcgtttctgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTAT

Basic information

species Zea mays
transcript GRMZM2G173195_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G173195_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os05g41590.1 (Oryza sativa), 3'ss of exon 3
gtttgtgctgccaacccaccatttggacaatgtgaagtttgcttaaatgccaggtgccttttgcttaaacgcttaggctatatgctgattcttatt-cgtttctgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTAT
      | ||     | ||| | |  |  |||| ||  || |   | | |  ||||  ||||   |   ||  ||| | || |||| |   ||  |  | || | |  | |||||||| ||||||||| ||||||||||||| ||  |||||||| | ||| |||||||||  |||||||||   ||||||  ||||||||| || ||||| |
------gttggtg--ctaccttcttaatgatgtaaatctttccatacttctgggtgtgtttttggtgc-cgaatag-ccatgtgctaagatttgctgtgattttatc-tttagGGTGTCTCTGCAGTCCATGCATTTTATGAGCTCTTGAGCCAGAGTAGCTTAAGCGTGACACATCCAGAAGTGAAGAAGCTTGTTGCTCCGGTCGAGCTGT
















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|71321152|gb|DR797273.1|DR797273
EST:     AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
genomic: AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
EST: gi|71321153|gb|DR797274.1|DR797274
EST:     AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCA
genomic: AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCA
EST: gi|211410040|gb|FL464376.1|FL464376
EST:     GGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
genomic: GGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
EST: gi|148950857|gb|EC896476.2|EC896476
EST:     AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
genomic: AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
EST: gi|74237979|gb|DT645893.1|DT645893
EST:     AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
genomic: AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
EST: gi|148946890|gb|EC892170.2|EC892170
EST:     AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
genomic: AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
EST: gi|4966995|gb|AI691780.1|AI691780
EST:     AACTGACTCTAGAAATGGGGGNCAGCATCAAGGGCAAAGGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
genomic: AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
EST: gi|211407489|gb|FL464375.1|FL464375
EST:     AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
genomic: AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
EST: gi|78023830|gb|DV492217.1|DV492217
EST:     AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAG                         GGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA
genomic: AACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTA

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: 90

ACTGCTGAAAGGTCGCAATGCATGGTATGGGCAGAAGTTAGCTAAGGGAGAACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 64

ACTGCTGAAAGGTCGCAATGCATGGTATGGGCAGAAGTTAGCTAAGGGAGAACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTAT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 89

ACTGCTGAAAGGTCGCAATGCATGGTATGGGCAGAAGTTAGCTAAGGGAGAACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTAT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 35

ACTGCTGAAAGGTCGCAATGCATGGTATGGGCAGAAGTTAGCTAAGGGAGAACTGACTCTAGAAATGGGGGACAGCATCAAGGGCAAAGGGACTATCCAGgtttgtgctg ... tgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTAT




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgcttaaacgcttaggctatatgctgattcttattcgtttctgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTAT
                         tgctgat  putative branch site (score: 35)
                               ttcttattcgtttct  CT-rich tract
                              attcttatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttgtgctgccaacccaccatttggacaatgtgaagtttgcttaaatgccaggtgccttttgcttaaacgcttaggctatatgctgattcttattcgtttctgtgatctagGGTGTTTCTGCAGTCAATGCATTTTATGAACTGCTGAGCCAGGGAAGCCTAAGCGTGATGCATCCAGAAACCAAGAAGGCTGTTGCTCCTGTTGAGCTAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT