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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctacatgaatctgcatgttgcacaatcgagatattctcatttcccccttttgccttttgatagtttgatatcacaaactgaatgcttggtcacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG

Basic information

species Zea mays
transcript GRMZM2G085577_T01
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 14
lower sequence: LOC_Os01g63270.1 (Oryza sativa), 3'ss of exon 14
ctacatgaatctgcatgttgcacaatcgag-atattctcatttccccctt-ttgccttttgatagt---ttgatatcacaaactgaatgcttggtcacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG
 | ||  || ||  ||||   |||| | |  | |    |||| | | ||| ||||  | || |  |    |||   |    | | ||| | || |    ||||||||||||||| || |||| ||||||||| ||  ||||||||||||| |||||||||||||| ||||| || || ||||| |||||||| ||||| ||||||
-tgcac-aacct--atgtgagacaaccaaacacaagaacattgcgctcttattgctatctgttcttgcactgaatgctttgattaaat-cctgtttctctgacagGGATAAGAAAAAATGGATCAAGATGTCTATACTGAACACAGCTGGAAGTGGCAAATTCAGCAGCGACCGTACTATCGCTCAGTATGCAAAGGAAATATGG

upper sequence: GRMZM2G085577_T01 (Zea mays), 3'ss of exon 14
lower sequence: Vv06s0004g06020.t01 (Vitis vinifera), 3'ss of exon 14
--ctacatgaatctgcatgttgcacaatcgagatattctcatttcccccttttgccttttgatagtttgatatcacaaactgaatgcttggtcacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG
   |   |  ||   | |     |       |   ||   || ||    || |    ||  | | |||| | | |    || ||   |   |  | || |||||||| ||| |  |||   |||||||| || |||| ||| |||||||||||||||||||| || ||||| ||||| || || || |||||||| || |||
ggttctttttatgcccctagctgaaggcaatggccttgcaatatcgtgtttctcaacttcaaca-tttgttctgaatttctaaaacatattttgcctg-cagGGATAGGAAAAGATGGCTAAAGATGTCTATATTGAGCACTGCTGGGAGTGGCAAATTCAGCAGTGATCGAACCATAGCTCAATACGCCAAGGAAATTTGG
















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|93283527|gb|EB675791.1|EB675791
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|211014837|gb|FL417332.1|FL417332
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|67041226|gb|CO467481.1|CO467481
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|71301961|gb|DR787056.1|DR787056
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|76924589|gb|DV170028.1|DV170028
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|22490823|gb|BU050746.1|BU050746
EST:     GACTTCCCAAGCTACATCGATGCACAGGACCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|32855932|gb|CD995613.1|CD995613
EST:     GACTTCCCAAGCTACATCGATGCACAGGACCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAG
EST: gi|211355999|gb|FL410711.1|FL410711
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|211215959|gb|FL334799.1|FL334799
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGGAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|60354851|gb|DN221824.1|DN221824
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|60354619|gb|DN221592.1|DN221592
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|16927694|gb|BM080763.1|BM080763
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|40335159|gb|CK369229.1|CK369229
EST:     GACTTCCCAAGCTACATCGATGCACAGGACCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTTGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|60347330|gb|DN214303.1|DN214303
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|32866201|gb|CF005883.1|CF005883
EST:     CGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCCGGGAGTGG
genomic: CGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|71301958|gb|DR787055.1|DR787055
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|60401276|gb|DN234083.1|DN234083
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|6636976|gb|AW261248.1|AW261248
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|211204436|gb|FL394622.1|FL394622
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGG
EST: gi|37380429|gb|CF627026.1|CF627026
EST:     GACTTCCCAAGCTACATCGATGCACAGGACCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTTGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|60348694|gb|DN215667.1|DN215667
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|211359734|gb|FL344672.1|FL344672
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|19770331|gb|BQ035052.1|BQ035052
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|71767179|gb|DR965116.1|DR965116
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|60340741|gb|DN207714.1|DN207714
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|89106551|gb|DY576768.1|DY576768
EST:     GACTTCCCAAGCTACATCGATGCACAGGACCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|19436465|gb|BM952875.1|BM952875
EST:     GACTTCCCAAGCTACATCGATGCACAGGACCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
EST: gi|211028797|gb|FL457634.1|FL457634
EST:     GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAA                         GGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG
genomic: GACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGG

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), 48 (downstream exon)
Score: 217

TTGAAGGGAATTCTGGATTTGGGCGTGGTGATTATTTCCTTGTTGGCTATGACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 223

TTGAAGGGAATTCTGGATTTGGGCGTGGTGATTATTTCCTTGTTGGCTATGACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG


Block sizes: 49 (upstream exon), 48 (downstream exon)
Score: 123

TTGAAGGGAATTCTGGATTTGGGCGTGGTGATTATTTCCTTGTTGGCTATGACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 266

TTGAAGGGAATTCTGGATTTGGGCGTGGTGATTATTTCCTTGTTGGCTATGACTTCCCAAGCTACATCGATGCACAGGATCGGGTGGATGCAGCCTACAAgtaagaacac ... cacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ccttttgccttttgatagtttgatatcacaaactgaatgcttggtcacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG
         ttttgata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctacatgaatctgcatgttgcacaatcgagatattctcatttcccccttttgccttttgatagtttgatatcacaaactgaatgcttggtcacatgacagGGATAAGAAGAAGTGGACCAAGATGTCCATCTTGAACACAGCTGGGAGTGGCAAATTCAGTAGCGATCGCACCATCGCCCAGTATGCCAAGGAGATATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
ctacatg
- - - - - -tgcatgt
- - - - - - - - - tgcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atcacaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaatgc