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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagagagggattgtgcagcattgtttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcag

Basic information

species Zea mays
transcript GRMZM2G030422_T04
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G030422_T04 (Zea mays), 5'ss of exon 4
lower sequence: LOC_Os03g14980.2 (Oryza sativa), 5'ss of exon 2
AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagta-gagagggattgtgcagcattg----tttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcag
|||||||||| ||||| || ||||||||||| || ||||||||||| ||||||||||||||||||||||| || ||||||||||| ||||| ||||||||||||||| | ||||||   ||   |        |||  ||  || |||||||  || || || ||   |||||| ||||||    |  |||
AGCGCTACCTCGGTGGCTTTACCAAGGTTGATGACAACCGCTACTCGATGAAGATATTCTTTGAGATCCGCAAACAGAAGTATCTTGAGGCCCTTGATAAgtaagtatgggagggaacatgtccctacaggaattttaggtgctggagtggaaagcgttgctaact--gggtttgtttgctgctctg-cag

upper sequence: GRMZM2G030422_T04 (Zea mays), 5'ss of exon 4
lower sequence: PP1S99_260V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagagagggat----tgtgcagcattgtttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcag------------
| || ||  |   ||| || || || || ||||| |||||||| |||||||| || ||||||||||| || |||||||||||| |||| ||||| |||||||| |||| ||    |     |||| |  |  ||| |  |||||||  | |   |   || ||  |  | ||| |||      ||  | |            
AACGATATTTATCTGGGTTTACTAAAGTCGACGACAACCGCTATTCCATGAAAATCTTCTTTGAGATTCGCAAGCAGAAGTATTTGGAAGCTCTGGATAAgtatgtagcgatttgtgccgcgtgcgggctcatttctaccacttgaa-gcaaaacacatcagatgaatg-tttgtttagaggaatggctgtgtcttggtttc

upper sequence: GRMZM2G030422_T04 (Zea mays), 5'ss of exon 4
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 5'ss of exon 2
AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagagaggga----ttgtgcagcattgtttatggcact-tgagtggagtgcctt--------tctgaccaggggtttctttgctttcata-tcag
| || ||  |   ||| ||||| ||||| || || |||||||| || ||||| || ||||||||||| ||||| || ||||| ||||| ||||| || ||||| |||   ||       | ||   |  |  ||   |  | | | ||  || | | ||        |||      |||      || | || |  | ||
AACGATATTTATCTGGGTTCACTAAGGTGGATGACAACCGCTATTCAATGAAAATCTTCTTTGAGATACGGAAACAAAAGTACCTGGAAGCTCTGGACAAgtacgtattcagttgcatctcgtttggagtcattggggtgattcttagcagactacattgatttaagtctcgttctgggggaagatgttatcttggttag

upper sequence: GRMZM2G030422_T04 (Zea mays), 5'ss of exon 4
lower sequence: EFJ36405 (Selaginella moellendorffii), 5'ss of exon 6
---------------------AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagagagggat-tgtgcagcattgtttatggcacttgagtggagtgccttt-----ctgaccaggggtttctttgctttcatatcag
                     || | ||| |   ||| ||||||||||| || || || ||||||||||||||||| ||||| |||||  | ||||| ||||| || |||||  | || | || |||    ||   | | |    |  | | | |  | |||   | |  |  || |     ||      | |    | ||  ||  |  |||
ATGGGGAGTGGGACGAGGTGGAGAGGTACTTGTCTGGCTTCACCAAGGTGGATGACAATCGCTACTCCATGAAGATTTTCTTGGAGATAAGAAAGCAAAAgtacctcgaggccttggacaggtgagtgactagttctctctctctctctctctctctctctttttttgcttttctcttatctcttgtggcgagccgatctgtgttgtttgcag

upper sequence: GRMZM2G030422_T04 (Zea mays), 5'ss of exon 4
lower sequence: EFJ32018 (Selaginella moellendorffii), 5'ss of exon 2
AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagagagggattgtgcagcattgtttatggcacttgag----tggagtgcctttctgaccagg---ggtttctttgctttcatatcag--------------------
|| | ||| |   ||| ||||||||||| || || || ||||||||||||||||| ||||| |||||  | ||||| ||||| || |||||  | || | || ||| || | |  || |    |  | ||| |  |  || |     |   |   || ||| | |  |   |||      | | | |||   |                    
AGAGGTACTTGTCTGGCTTCACCAAGGTGGATGACAATCGCTACTCCATGAAGATTTTCTTCGAGATAAGAAAGCAAAAGTACCTCGAGGCCTTGGACAGgtgagt-gacaagttttctctttctctctttctctctttttatgttttcttgcttctctcttatctcgtgtggtgagccagttctgataaggggggctctgtgttgtttgcag

upper sequence: GRMZM2G030422_T04 (Zea mays), 5'ss of exon 4
lower sequence: EFJ37833 (Selaginella moellendorffii), 5'ss of exon 2
AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagagagggattgtgcagcattgt---ttatggcacttgagtggagtgc-ctttctgaccaggggtttctttgctttcatatcag--------------------
|| | ||| |   ||| ||||||||||| || || || ||||||||||||||||| ||||| |||||  | ||||| ||||| || |||||  | || |||| ||| || | |  || |    | || |   || |     ||   ||     | |||| |  |  | |||      | | | |||   |                    
AGAGGTACTTGTCTGGCTTCACCAAGGTGGATGACAATCGCTACTCCATGAAGATTTTCTTCGAGATAAGAAAGCAAAAGTACCTCGAGGCCTTGGACAAgtgagt-gacaagttttctctctctttctctctttttatgtttttttgcttctctctttatctcgtgtggtgagccagttctgataaggggggctctgtgttgtttgcag

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|24769219|gb|CA404348.1|CA404348
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTCGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|19058337|gb|BM737004.1|BM737004
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|76288699|gb|DV028267.1|DV028267
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|18655046|gb|BM499851.1|BM499851
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTGGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCT
EST: gi|18662061|gb|BM501725.1|BM501725
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|71766923|gb|DR964860.1|DR964860
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|74034831|gb|DT535322.1|DT535322
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|211301796|gb|FL438950.1|FL438950
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|18662063|gb|BM501726.1|BM501726
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
EST: gi|18655047|gb|BM499852.1|BM499852
EST:     AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAA                         GCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT
genomic: AAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTT

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: 149

AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 53

AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 45

AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 106

AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagag ... ttcatatcagGCATGATCGGTCAAAGGCTGTTGAAATCTTGGTCAAGGACCTTAAGGTCTTTGCATCCTTCAATGAGGAGTTGTTCAAGGAGATCACACAGCTTCTAACC


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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGCGCTACCTTGGTGGATTCACCAAGGTTGACGATAACCGCTACTCCATGAAGATATTCTTTGAGATCCGGAAGCAGAAGTATCTGGAGGCTCTTGATAAgtaagtagagagggattgtgcagcattgtttatggcacttgagtggagtgcctttctgaccaggggtttctttgctttcatatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG