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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactccccttagatacaatcatcatttaacattttttagataatttcctttgggtaaattaatgcatatatggtttctactttgagaagcacttatggt...

Basic information

species Zea mays
transcript GRMZM2G155837_T01
intron # 14
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g52630.1 (Oryza sativa), 5'ss of exon 16
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactccccttagatac-aatcatcattt-aacattttttagataatttcctttgggtaaattaatgcatatatggtttctactttgagaagcacttatggt-------------
||| ||||||||||||| ||||||||||||||||||||||| ||||||||||||||||||||||| |||||  | ||||| ||| |||||  ||  ||||||||||||||||  ||| ||||||  ||| || ||  ||  |||   |    | |||| || || ||||| ||    || ||   | | |  |  || |  |             
TTTGTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGCTGCATTCCTGCTCAAGGCTACTATGGGCCCTCTATCTCGGCTCTGAGTTTAAAACCAAgtactccccttaactacgaatcatggtttcaatatgattatgatttatattctggggtcaactattgcatttaa---ttgtaagatcacattcttttctcttgtcttcctgttag

upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g52600.1 (Oryza sativa), 5'ss of exon 18
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTC---CAAgtactccccttagataca-atcatcattt-aacattttttagataatttcctttgggtaaattaatgcat----------atatggtttctactttgagaagc--acttatggt---
   |||||||||||||| ||||||||||||||||||||||| |||||||||| |||||||||||| |||||  | ||||| |||||||||| ||| |   || |||||| |||||  || | || ||  ||  || ||      |||   ||   | |||| | ||    |||          ||    ||| |  | | | |||   |||| | ||   
---CTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGCTGCATTCCTGGTCAAGGCTACTATGGGCCCACTATCTCGGCTTTGAGTGTAACCCCTGCAGgtactcaccttaactatagataatggttccaatatgaaaatgatgtattttctagggtcagttgtaccattctgcctaagatcacattttttttctaacaagtgaacttcttgtcag

upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g52614.1 (Oryza sativa), 5'ss of exon 14
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCC---AAgtactccccttagatacaatcatcatttaacattttttagataatttcctttgggtaaattaatgcatatatggtttctactttgagaagcacttatggt
   |||||||||||||| ||||||||||||||||||||||| ||||||||| ||||||| ||||| |||||  | ||||||||| |||||| ||  ||   | |||| |||||||  |||||  |||||       |    ||||   ||   | |                                               
---CTTGAGATTCATCTCTTCTGGGCTGGCAAGGGCACTTGCTGCATTCCTACTCAAGGATACTATGGGCCCACTATCTCAGCTCTGAGTGTAATCCCTGCAGgtaccccccttaactacaa--atcat-----ggtcccaagatggattttctag-----------------------------------------------

upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g52640.2 (Oryza sativa), 5'ss of exon 17
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactccccttagatacaa-tcatcatt-taacattttttagataatttccttt---gggtaaattaatgcat--------------atatggtttctactttgagaagcacttatggt-----
||  ||||||||||||| ||||||||||||||||| ||||| ||||||||| ||||||| ||||| |||||  | ||||||||| |||||  ||  ||||||| ||||||||  ||||| |||||||  |  || | |  | |  || |  |||   |||| || |  |||||                ||  ||| | ||   ||  | |||| |  |     
TTCGTTGAGATTCATCTCTTCTGGGCTGGCAAGGGAACTTGCTGCATTCCTACTCAAGGATACTATGGGCCCACTATCTCAGCTCTGAGTTTAAGCCCAAgtattccccttaactacaaatcatcatggttccagtatgaaaacgatgtattttctagggttaactgttgcattccattgtaagattgcatttttttttctaacaggtgaactttttttgttag

upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: LOC_Os04g52606.1 (Oryza sativa), 5'ss of exon 4
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCC---AAgtactccccttagatacaat-catcatttaacattttttagataatttcctttgggtaa------attaa--tgcatatatggtttctactttgaga-agcactt-atggt---------------------
    ||||||||||||| ||||||||||||||||| ||||| ||||||||| |||||| | | || |||||  | ||||| ||| |||||  ||  ||   | ||||||| || |   ||||| |||  ||   ||||||  | | ||| |  |||  || |      ||| |  | |||    ||  |  | | | ||| | || || ||  |                     
---GTTGAGATTCATCTATTCTGGGCTGGCAAGGGTACTTGCTGCATTCCTACTCAAGACAATTATGGGCCCTCTATCTCGGCTCTGAGTTTAATCCCTGCAGgtactcctctgaacaacaattcatggttc--cattttgaaaacaatgtattttcagtgatcaactattgagtttcattgtaggccttcattgtaagataacattttattctaacaaatggacttcttttcag

upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA08G25590.1 (Glycine max), 5'ss of exon 20
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactccccttagatacaatcatcattta-acattttttagataa--tttcctt-tgggtaaattaatg-catatatggtttctactttgagaagcacttatggt--------------------------
| ||||||||||||||| || |||||||| || || ||||||||||| ||  |||||||    || |||||   |||   |||  |   ||| | |||| ||| | |  | | | | | |  | ||||| |  |||  |   |||  |||| || ||  |||     |  ||  ||    ||| |  || | |     || |  |                          
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATTCCAGgtaatactatgaaaaaaattggtaatttagatgtttaattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatttttttaatttgatacattgttttgtgttgtacag

upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: GLYMA08G25600.1 (Glycine max), 5'ss of exon 17
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactccccttagatacaatcatcatttaacattttttagataatttcctttgggtaaat-taatgcatatatggtttctactttgagaagcacttatggt--------------------------------
| ||||||||||||||| || |||||||| || || ||||||||||| ||  |||||||    || |||||   |||   |||  |   ||| |  ||| ||| | |  | | | | | |    | || | || ||| |  || |  |||||   ||    |||| | |     | |     ||  | |   |  |||  |                                
TATCTTGAGATTCATCTCTTTTGGGCTGGAAAAGGTACTTGTTGCATACCAACTCAAGGTACTTATGGGCCCTTAATTCAAGCAATCCATGCTATCCCAGgtaatactatgaaaaaaatttggtaatttagatgttt-aattactaacctttcattatgcataatcccttatcagctagatattcaaaatttatatatatttttaatttgataaattgttttgtgttgtacag

upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: AT1G56145.2 (Arabidopsis thaliana), 5'ss of exon 18
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactccccttagatacaatcatcatttaacattttttagataatttcctttgggtaaattaatgcatatatggtttctactttgagaagcacttatggt
|  |||||  ||||||||||||||||||| || || || || || |||||||||||||||   || |||||   | |||||||| | |||||||||||| |||       || |||||  ||  |  |  |||  | |   ||   |||  ||  |    |||    ||   || || || | |  | ||          
TACCTTGAAGTTCATCTTTTCTGGGCTGGAAAAGGGACCTGCTGTATTCCTGCTCAAGGCACTTATGGGCCATTAGTCTCAGCTATCAGTGCAACTCCAGgta-------tacatacag-cagaaactttcatgatcttcgtagagtccaatgtatcttctaac---ta-gcggcttttattctctgcag----------

upper sequence: GRMZM2G155837_T01 (Zea mays), 5'ss of exon 14
lower sequence: Vv00s0125g00210.t01 (Vitis vinifera), 5'ss of exon 2
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactccccttagat-acaatcatc-----------atttaacattttttagataatttcctttgggtaaattaatgcatatatggtttctactttgagaagcacttatggt
| |||||| |||||||| ||||||||||| ||||| ||||| ||||| |||  | | || || || || ||  | || |||||  | ||||    | || |||  ||  ||| || | | | ||            || ||| || |  |   |  |     ||  |  || |    |  |  ||||| ||  |||     || |       
TATCTTGAAATTCATCTGTTCTGGGCTGGTAAGGGAACTTGCTGCATACCTTATGATGGTTATTATGGACCATCCATTTCAGCCCTCAGTGTTGTTTCAGgtaacccatttaaatgatagttatagaattcatataatataagatgtcctgactggtgcttcttttgccaactgcaactgaattggttgctgatttattttgctcag-----

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|18383718|gb|BM416918.1|BM416918
EST:     TGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAA                         ATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGA
genomic: TGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGA




















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: 48 (upstream exon), 46 (downstream exon)
Score: 51

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 145

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 132

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 97

TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactcccct ... tttctcacagATTTTACCCCTACAGTGCGTAATTCTGCACAGAAGAAGAACAGTAGTAAAACAGGTGTAATTGTTGGGGTTGTGATTGGTGCAGCAGTTTTAGGAGTACT


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTTCTTGAGATTCATCTTTTCTGGGCTGGCAAGGGCACTTGTTGCATTCCTGCTCAAGGCTACTACGGGCCTGCAATCTCAGCTTTGAGTGCAACTCCAAgtactccccttagatacaatcatcatttaacattttttagataatttcctttgggtaaattaatgcatatatggtttctactttgagaagcacttatggt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT