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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ttatggtgctgtatgcttaattcttgtctttcccggcttcatcaaattgctctttttctgcattgtgctgtttcagtttactgatttaaatgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA

Basic information

species Zea mays
transcript GRMZM2G458208_T01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os10g32550.1 (Oryza sativa), 3'ss of exon 6
---------------------------ttatggtgctgtatgcttaattcttgtctttcccggcttca--tcaaattgctctttt-tctgcattgtgctgtttc---agtttactgatttaaatgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA
                           ||    |    |||   || ||  |   |   |   ||| |  | ||| ||  ||| |  |  || | || | ||||   | |||  |   |||||  ||   ||||| |||||||||||||| |||||||||||||||||||| || |||||||| |||||||| ||||||||||| |||||  |||||||| |||| |||||||
gtaagttgatccaagttaaaactgaacttggcctctcttatctctatttggttggtagacttcctttagttaaaactgaacttgtgccaacactctggtttttcgttaatttgtttgcttaaacatttggtagGATGGTAACACCCTTTACAATGAGCTTGAAGTTGTGGAAGGCATGAAACTTGACAGAGGCTACATCTCTCCTTACTTTGTTACCAACCCAAAGACCCAGA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 5
lower sequence: AT2G33210.1 (Arabidopsis thaliana), 3'ss of exon 5
ttatggtgctgtatgcttaattcttgtctttcccggcttcatcaaattgctctttttctgcattgtgctgtttcagtttactgatttaaatgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA
          ||  | | |||| |     | ||    |   |||||||  | |  || | | ||  | ||    |  |||     |      |  || |||| || || ||| | | ||||||||| |||||||| |||||||||||  | ||||| || |||||||| ||||||||||| || ||| | ||||| || |
----------gtgagttgaatttta----tccctaaat--gtcaaattattttgcttattccttaaggtgaccaatgttatcatctct----tgattcagGATGGCAAGACCTTGTTTAATGAGCTGGAAGTTGTTGAGGGTATGAAGATTGACAGGGGATACATCTCCCCGTACTTCATAACTAACCCGAAAACACAAA

upper sequence: GRMZM2G458208_T01 (Zea mays), 3'ss of exon 5
lower sequence: PP1S378_9V6.2 (Physcomitrella patens), 3'ss of exon 6
ttatggtgctgtatgcttaattcttgtctttcccggcttc--atcaaattgctctttttctgcattgtgctgtttcagtttactgatttaaatgttcttt--agGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA
   ||       || |  ||||  ||  ||   || ||    ||   || | |   |   ||||   |  || | | ||  |  ||     | |||| ||  ||||||| || || || | ||||||| | || ||||||||||||||||| || |||||||| || |||||||| || ||||| ||||| || || || || |
--ttgaaataagatacc-aatttgtgcattatacgcctcaggatatgatagataagtgaatgcaacctagtgctcccgtg-atggacggttacgttccttgcagGACGGAAAAACTCTGTTTAATGAGTTGGAGGTTGTGGAGGGTATGAAGCTCGACAGAGGATATATCTCTCCCTATTTCATCACCAATTCTAAGACTCAAA

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|33101516|gb|CF061476.1|CF061476
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|33102191|gb|CF062151.1|CF062151
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|31357599|gb|CD441956.1|CD441956
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTG
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|61119163|gb|DN560124.1|DN560124
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|13388799|gb|BG462407.1|BG462407
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|31361464|gb|CD445821.1|CD445821
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTG
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|88747169|gb|DY531310.1|DY531310
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|5499101|gb|AI854968.1|AI854968
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|31349389|gb|CD433746.1|CD433746
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTG
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|67016113|gb|CO444862.1|CO444862
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAATTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|94476466|gb|EB705424.1|EB705424
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|67023196|gb|CO451945.1|CO451945
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAATTA
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA
EST: gi|31355665|gb|CD440022.1|CD440022
EST:     TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCG                         GACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTG
genomic: TTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTA

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: 492

GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 277

GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 180

GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 336

GTGGGTACAATATCAGCAAATGGGGAAAGGGAAATTGGTGAGCTTATTGCCAAGGCTATGGAGAAGGTTGGCAAAGAGGGTGTCATCACTATTGCGgtaagttaaa ... tgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgctctttttctgcattgtgctgtttcagtttactgatttaaatgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA
                                 tactgat  putative branch site (score: 336)
                                             tgttcttt  putative PPT
                                      atttaaatgttcttta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ttatggtgctgtatgcttaattcttgtctttcccggcttcatcaaattgctctttttctgcattgtgctgtttcagtttactgatttaaatgttctttagGACGGTAACACCCTTTATAATGAGCTTGAAGTTGTGGAGGGTATGAAACTAGACAGAGGTTACATCTCTCCGTACTTCATTACCAACTCAAAAACCCAGA

- - ggtgctg
- - - - - - -tgcttaa
- - - - - - - - - - ttcttgt
- - - - - - - - - - - - - - - - - - cttcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -actgatt