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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatttgttccttttattttcatatatattgtatccctttgcattgtctccgattacctcttgcatcagatggcagtgctatattctcttgaaaatcagaagtgatgtcaatactcatattttttcaatcttttattttttattgtcactcacaattttttttgtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG

Basic information

species Zea mays
transcript GRMZM2G124886_T04
intron # 22
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G124886_T04 (Zea mays), 3'ss of exon 22
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 3'ss of exon 13
gtatttgttccttttattttcatatatattgtatccctttgcattgtctccgattacctcttgcatcagatggcagtgctatattctcttgaaaatcagaagtgatgtcaatactcatattttttcaatcttttattttttattgtcactcacaattttttttgtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG
                                                            | || |||  ||  |   | ||||  |     |||| |||||| |||||  | ||||| | | ||       || || ||||||||  || |  |  |  |  |||||||||||| ||| |||||||| |||||||||||||| || |||||||| ||| | ||||||| | | ||||||||||| ||||  |||||| ||||   ||||  |
------------------------------------------------------------tagcttcaattg--aacac-atatagtgaaataaat-agaagtaatgtcggtgctcatttgtattg------tttttctttattgtt-ctgatgaaatcct--gtttgaatagGGGTATTTATCCACCAGCTGAGGAGTACATTATCCATGCTGAGAGGCCCAATGAGACTCTGGTGGAAGCTTTCAAAAGTATGCATATACATCTAGAGGAG
















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|32794634|gb|CD946870.1|CD946870
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCCCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|211291669|gb|FL235609.1|FL235609
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCCCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|67014399|gb|CO443148.1|CO443148
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19822105|gb|BQ048129.1|BQ048129
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19822050|gb|BQ048074.1|BQ048074
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|26455841|gb|CA827424.1|CA827424
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19821970|gb|BQ047979.1|BQ047979
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|5847331|gb|AW000410.1|AW000410
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGGTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|111145650|gb|EE257974.1|EE257974
EST:     AGACTGGCAGATTNGCTCTGAATGTAAAAACCTGCTGTTGCCCCGAAAAG                         GGTTATCTATCC
genomic: AGACTGGCAGATT-GCTCTGAATGTAGAAGC-TGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCC
EST: gi|19822070|gb|BQ048094.1|BQ048094
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19822158|gb|BQ048182.1|BQ048182
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|19821973|gb|BQ047982.1|BQ047982
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
EST: gi|26456008|gb|CA827591.1|CA827591
EST:     GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAG                         GGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA
genomic: GAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAA

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), 49 (downstream exon)
Score: 150

CAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 235

CAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 329

CAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 237

CAAAAGCAGCGGAGTCCCTGGCTGATCCTAATGAGTACCCAAACTTATTTGAAGACTGGCAGATTGCTCTGAATGTAGAAGCTGCTGTTGCTCCGAAAAGgtatttgttc ... gtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attttttcaatcttttattttttattgtcactcacaattttttttgtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG
                            cactcac  putative branch site (score: 237)
                                     ttttttttgttt  putative PPT
     ttcaatcttttatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatttgttccttttattttcatatatattgtatccctttgcattgtctccgattacctcttgcatcagatggcagtgctatattctcttgaaaatcagaagtgatgtcaatactcatattttttcaatcttttattttttattgtcactcacaattttttttgtttgaatagGGTTATCTATCCACCGGCTGAGGAGTACATGATTCATGCTGAAAGGTCAAATGAGAATTTAGTGGAAGCTTTTAAAAACATGCATGTACAGGAAGAGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG