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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatccgagtaatatgcgcatattgagatttcattctggatgcaataccaatctttgctatcgataccttttctatacctagttttacttgattc...

Basic information

species Zea mays
transcript GRMZM2G316967_T01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 13
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 5'ss of exon 13
GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatccgagtaatatgcg------catattgagat-ttcattctggatgcaataccaatctttgcta----tcgataccttttctatacctagtt-ttacttgattc------------------------------------------------------------------------------
|| ||||||||||||||||| ||| | ||  |||||||||||||||||||||| |||||||| || || || || ||||||||||||||||||||| ||| || ||  |  ||  |      |   ||| | |  | ||| |  | || | || | |  ||   |    |  | |    |  ||| | |  || ||| |   | |                                                                              
GTCTGGGATATGCATGGACAGAAACTGTTTTCATTTGAAGGGCATGAGGCACCAGTGTATTCCATCTGCCCTCACCACAAAGAGAGTATTCAGgtgggttttctgaacagaatatgatatttccagttgtggtgcttattttataagctaaacaatttcttctcaagattgaacagaggtagtatgcgtgattattaatgtgtccattcagtaaaaaaggggctgtctaatgttattaatgtcgatttcttgtgttgatgtgctattcttatgttccctgaag

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA19G41840.2 (Glycine max), 5'ss of exon 13
GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatccgagtaatatg-cgcatattgagatttcattctggatgcaataccaatctttgctatcgataccttttctatacctagttttacttgattc-
|| |||||| |   |||||  ||| |||| |  ||||| ||||||||||||||||| |||||||| ||||| |||||||||||||| ||||||||            | || ||     | ||  |  || |||||        |   | |  |   |   ||||   | ||  |   || |||||| |   |  
GTCTGGGATTTAACTGGACGGAAACTATTTAACTTTGAGGGGCATGAGGCACCTGTATATTCTATCTGTCCTCATCACAAAGAGAGCATTCAGgtacagagatgatatgatgtgatttgttttctgtgtttattctttggattttgtaagttataatt--tgatagactatcactctataattttacctatgtgc

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA10G29090.1 (Glycine max), 5'ss of exon 14
GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgt---gttatccgagtaatatgcgcatattgagatttcattctggatgcaataccaatctttgctatcgataccttttctatacctagttttacttgattc-
||||||||| |  ||||||  ||| ||||| | ||||| ||||| || |||||||||||||| || ||||| |||||||||||||  ||||||||     ||        | ||    |||| |  |  ||||| | |  || |  |   ||  ||| ||  | |||     | |     ||  |||| |  |||| 
GTATGGGATTTAAATGGACGAAAACTATTCTCCTTTGAGGGGCACGAAGCACCTGTGTATTCCATTTGTCCCCATCACAAAGAGAACATTCAGgtacaaagtagatatcattattgaggcatctataattttcaatgtttattctttgg-aaggttttctgcc-atattccatttgctatta--tttaataaattcg

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA20G38230.1 (Glycine max), 5'ss of exon 14
GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatccgagtaat-atgcgcatattgagattt-cattctggatgcaataccaatctttgctatcgataccttttctatacctagttttacttgattc
||||||||| |  ||||||  ||| ||||| | ||||| || || || |||||||||||||| || ||||| |||||||||||||  |||||||||     |     | || ||      ||  | |||| || | |  || |  |   |   |||       || ||  ||  ||   ||| || | |   || 
GTATGGGATTTAAATGGACGAAAACTATTCTCCTTTGAGGGCCACGAAGCACCTGTGTATTCCATTTGTCCCCATCACAAAGAGAACATTCAGgtgcaaagtagatatcattattgaggcatctatattttcaatgtttattctttggaaggttttctgccatattccacttaaattagtaggtt-attcagtt-

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 13
lower sequence: GLYMA03G39290.1 (Glycine max), 5'ss of exon 14
GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatccgagtaatatgcgcatattgagatttcattctggatgcaataccaatctttgctatcgataccttttctata--cctagttttacttgattc
|| ||||||||   |||||  ||| |||| |  ||||| |||||||||||| |||| |||||||| ||||| |||||||| ||||| ||||||||            | |||||        ||| ||    | |||||    ||        |   || |||   |  ||||||    ||  | | |       
GTGTGGGATATAGCTGGACGGAAACTATTTAACTTTGAGGGGCATGAGGCAGCTGTATATTCTATCTGTCCTCATCACAAGGAGAGCATTCAGgtacaaagatgatatgatatgttttctccgagtttattctttggattttgtaagttataatctgatggattgttcctctataattttacctatgcacaga--

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 13
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 5'ss of exon 13
GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatccgagtaatatgcgcatattgagatttcattctggatgcaataccaatctttgctatcgataccttttctatacctagttttacttgattc---
|| ||||||||| | ||    ||| |||| |  |||||||| |||||||| || || |||||||||||||| |||||||| ||||| ||||||||   | |    |   |   |    | |||    || | |    ||||| |     | | | ||| | | |   |  | |    |||||||| || || |   
GTCTGGGATATGAACGGGAGGAAACTATTTAATTTTGAAGGTCATGAGGCTCCAGTATATTCTATATGTCCCCATCACAAGGAGAGCATTCAGgtaaatcagttaaaacaagaggttttgttggttgttaactt---atgcatttgatgtttattctaacaaaagtgtgccaagtattagttttaatttatcccat

upper sequence: GRMZM2G316967_T01 (Zea mays), 5'ss of exon 13
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 13
GTATGGGATA-TGCAT--GGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatccgagtaatatgcgcatattgagatttcattctggatgcaataccaatctttgcta---------tcgataccttttctatacctagttttacttgattc
|| ||||||  ||||   |||| |||   || ||| |||||||| ||||| ||||||||||| ||| | ||||| ||||| |||||||||||||||||  | | |  |  |  || |    |  |    |||| |||    ||||       | || | ||         | ||| |||||| | | |  |   |||        
GTTTGGGATGCTGCAACAGGACGTAAGCAATACACTTTTGAAGGACATGAAGCACCTGTGTACTCTGTTTGTCCTCATCATAAAGAGAGTATTCAGgttggatttttgtatt-tacgttatttctctcctttccttc--actgcatcggtgttgttgggtaagaaatgtgtggatgccttttatgtgctgaaaattaac------

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|6021011|gb|AW065939.1|AW065939
EST:     AGAGTATTCAG                         TTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGAC
genomic: AGAGTATTCAGgtgtgttatc ... tttgatgcagTTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGAC
EST: gi|32865226|gb|CF004908.1|CF004908
EST:     ATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAG                         TTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGAC
genomic: ATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatc ... tttgatgcagTTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGAC

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: 174

GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatc ... tttgatgcagTTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 158

GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatc ... tttgatgcagTTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 178

GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatc ... tttgatgcagTTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 118

GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatc ... tttgatgcagTTCATCTTCTCAACTTCCCTTGATGGAAAAATTAAGGCCTGGCTTTATGACAATATGGGATCTAGGGTGGACTACGATGCTCCTGGCAAGTGGTGTACTA


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTATGGGATATGCATGGACATAAATTATTCACATTTGAAGGGCATGAGGCACCTGTGTATTCTATATGTCCGCATCACAAAGAGAGTATTCAGgtgtgttatccgagtaatatgcgcatattgagatttcattctggatgcaataccaatctttgctatcgataccttttctatacctagttttacttgattc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA