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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggatttttccccttctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA

Basic information

species Zea mays
transcript AC149818.2_FGT004
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AC149818.2_FGT004 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os03g05300.1 (Oryza sativa), 3'ss of exon 2
gtaaacgcctgcagttccacctgcatttatgttga-ttgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggatttttccccttct-cttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA
|||| |  |   |  ||||  | ||||  ||| || | |||||| ||    ||||| | | ||   ||||   ||  |||   ||  ||  ||||| |||||||  |     || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||| |||
gtaaccttcaagatctccaaatacattcgtgtagaatcgcgttcctg----gttggatcgattcgttgat---tgtctga---ttggggaatgggggtttttccgatggggtttatttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGGCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGCTCA

upper sequence: AC149818.2_FGT004 (Zea mays), 3'ss of exon 2
lower sequence: AT2G27960.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggatttttccccttctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA
                      |  ||  || | |     || | | | | |  |||  |  ||||  | |   | || |||  ||||||  |    |       ||      || | ||||||| ||||| ||||| ||||||||||| |||||||| ||||| || |||||| | || || || ||||||||||| ||||| ||| |  | ||  | |
-------------------taaggtttagtgataaagagattttagacatttgtgttgtgcaatctc-ttcaatgttgtattgattggtggtgatggtaaaaatgtttggaatttcgaagAACGAATGGCGAGCGATAGGAGTGCAGCAAAGCCGCGGATGGGTACATTACGCGGTTCATCGACCTGAGCCGCACATAATGCTATTCAGGAGGCCTCTTA

upper sequence: AC149818.2_FGT004 (Zea mays), 3'ss of exon 2
lower sequence: Vv06s0061g00810.t01 (Vitis vinifera), 3'ss of exon 3
gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggatt--tttccccttctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA
               ||   |||| | ||    |  |||| | ||   || |||     |  |    |    |  ||   || |   |        ||  | |    ||   ||  || ||||| || ||||| || || || || ||||||||||| |||||||| ||||| || || || ||||| ||||| ||||||||||| ||| |  | ||  | |
--------------ctctttctgcttctaaacag--tgcggtttt-ttctattgaaaaagaaa---aaaatttcaatc--ttctgcagccctaaagttgatattttgttgggttgatttcagAATGAATGGCGTGCTATTGGGGTTCAGCAGAGCCGTGGGTGGGTCCACTATGCAATTCATCGCCCTGAGCCACACATCATGCTCTTCAGGAGGCCTCTGA

upper sequence: AC149818.2_FGT004 (Zea mays), 3'ss of exon 2
lower sequence: EDP06083 (Chlamydomonas reinhardtii), 3'ss of exon 2
gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggattt--ttccccttctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA
                              ||     | | |  ||    |  ||  |   |||  |   ||||    || ||     |      || |  | ||||    |||   |||||||||||||||||||  | || |||||||||   || || ||||||||||||||||| ||||| || ||||| || |||||||||||| |           
------------------------------gtgaggcgtgcttatgata-gacggcattcctatgcg-cccctgcgccaacttcgcctttaaactatctcatcccccgctgctttcctgcagAACGAGTGGCGCGCTCTGGGCGTGCAGCAGTCGCGTGGCTGGGTGCACTACGCGATTCACCGACCAGAGCCACATATCATGCTGTTCAG-----------

upper sequence: AC149818.2_FGT004 (Zea mays), 3'ss of exon 2
lower sequence: PP1S7_399V6.2 (Physcomitrella patens), 3'ss of exon 3
gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggatttttcccct-tctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA
                     |||| |    |||    | |  ||  |  | || |||  | | |  ||   |  ||  ||||     | |     ||      || |    |   | |||   || |||||||  |||||||| |||||    ||||||||||||||||| || || ||||| || ||||||||||||||||| |||||| | ||  |||
--------------------atgcactgtcattgtcaacataattatcgggatgcttttatca-cgaatatatttatagatttcggcttttactcgttgcctaactatagactgaatacagGCTGAATGGCGCGGAATCGGAGTCCAGCAATCACGCGGGTGGGTGCACTATGCAATTCACCGACCTGAGCCGCACATCATGCTCTTCCGCAGACCCCTCA

upper sequence: AC149818.2_FGT004 (Zea mays), 3'ss of exon 2
lower sequence: PP1S36_271V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaatttt-ttggtgtggggatttttccccttctcttctttg-cagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA
                  ||  |  ||   |||| |  | | |     |  |   | | ||||||   | | || | | |||   ||     | |  |||  | || |    | |    |||  ||| ||||| |  |||||||||||||||   || |||||||| |||||||| || |||||||| ||||| ||||| ||||| |||||  | ||  | |
-----------------tacaggtcttgcagttggt--cctccgaatgccatcactattgttatc---ttcttgaacgcattacattaactcgcgtgtttcgctccctggaatttacaacagGCCGAATGGCGTGGTATCGGAGTGCAGCAGTCACGTGGGTGGGTTCACTACGCAATTCACCGCCCTGAGCCACACATTATGCTCTTCCGTAGACCCCTGA

upper sequence: AC149818.2_FGT004 (Zea mays), 3'ss of exon 2
lower sequence: EFJ28856 (Selaginella moellendorffii), 3'ss of exon 2
gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggatttttccccttctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA
                                                      |||||  |   |  |   || ||   |||||  |  |       ||      ||||   |||  ||||||| ||| |  | || ||||||||||||    | || ||||| ||||||||||| ||| | |||||||||||||||||||| ||  |  | ||  | |
----------------------------------------------------gtgtttgcgttcttcttctttgcatttgttttt--gcttaacccgcttgttttctctcaaatttctagAACGAATGGAGGACAATTGGAGTGCAGCAGTCTAGAGGCTGGGTTCACTACGCGATTCACAGACCGGAGCCGCACATCATGCTCTTTAGAAGGCCTCTAA

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: 1016

GCACGTCGTCCTCCCGCCCGAGGTCGCCAAGCTCCTCCCCAAGAACCGCCTCCTGTCCGAGgtaaacgcct ... ttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 120

GCACGTCGTCCTCCCGCCCGAGGTCGCCAAGCTCCTCCCCAAGAACCGCCTCCTGTCCGAGgtaaacgcct ... ttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 244

GCACGTCGTCCTCCCGCCCGAGGTCGCCAAGCTCCTCCCCAAGAACCGCCTCCTGTCCGAGgtaaacgcct ... ttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 253

GCACGTCGTCCTCCCGCCCGAGGTCGCCAAGCTCCTCCCCAAGAACCGCCTCCTGTCCGAGgtaaacgcct ... ttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgatgcctggatgaattttttggtgtggggatttttccccttctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA
 atctgat  putative branch site (score: 253)
                               tttttccccttctctt  putative PPT
          atgaatttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaacgcctgcagttccacctgcatttatgttgattgcgttcttgccctgttggtttggttatctgatgcctggatgaattttttggtgtggggatttttccccttctcttctttgcagAACGAGTGGCGCGCGATCGGAGTGCAGCAGAGCCGCGGGTGGGTGCACTACGCGATCCACCGCCCGGAGCCGCACATCATGCTGTTCCGCCGCCCGATCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT