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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgcgttcccctgcgcgcctgtctgattcaccctgaccctgtgattcctgtgtgaacaatttggctggttggaccttatttgtgtgctcgtgttgcatgttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG

Basic information

species Zea mays
transcript GRMZM2G101596_T01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G101596_T01 (Zea mays), 3'ss of exon 1
lower sequence: LOC_Os07g14580.1 (Oryza sativa), 3'ss of exon 1
gtgcgttcccctgcgcgcctgtctgattcaccctgaccctgtgattcctgtgtgaacaatttggctggttggaccttatttgtgtgctcgtgttgcatgttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
||  | |  | |    |  | | || |    | |      |||  ||  |  ||      |||| |   ||   | | |   | ||  |   ||   |||  | |||||||||||||||| ||||||||||||||||| || ||||||||
gtaagatggctttt-tgtttttttgttatctcttcgattcgtggctc--ggttgcttcgcttggttatgtgcttcatgtcgatttggcctgatttgttgtcgt-tgcagAGCCGGAAGGATGTGGAGGGGTCGCTCTTCGTTGTCAAGAG
















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|211391322|gb|FK987371.1|FK987371
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|93282402|gb|EB674666.1|EB674666
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393952|gb|FK987388.1|FK987388
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|37419345|gb|CF647353.1|CF647353
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|13125936|gb|BG316611.1|BG316611
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393945|gb|FK987381.1|FK987381
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|91056521|gb|EB166939.1|EB166939
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211391326|gb|FK987375.1|FK987375
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393953|gb|FK987389.1|FK987389
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393946|gb|FK987382.1|FK987382
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|76928738|gb|DV171746.1|DV171746
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|93281394|gb|EB673658.1|EB673658
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393955|gb|FK987391.1|FK987391
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|76010496|gb|DT937666.1|DT937666
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|7304674|gb|AW600613.1|AW600613
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393947|gb|FK987383.1|FK987383
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211391329|gb|FK987378.1|FK987378
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|76909432|gb|DV163378.1|DV163378
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|91048464|gb|EB158882.1|EB158882
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211391330|gb|FK987379.1|FK987379
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|76011730|gb|DT938900.1|DT938900
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|89758076|gb|DY687416.1|DY687416
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393949|gb|FK987385.1|FK987385
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211391323|gb|FK987372.1|FK987372
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|148930679|gb|EC872906.2|EC872906
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCACCCAGTGG                         AGCCGGACGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393951|gb|FK987387.1|FK987387
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|149112671|gb|EE191401.2|EE191401
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|148999366|gb|EE036307.2|EE036307
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393954|gb|FK987390.1|FK987390
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|211393950|gb|FK987386.1|FK987386
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
EST: gi|78114665|gb|DV533053.1|DV533053
EST:     CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGG                         AGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
genomic: CCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG

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: 22 (upstream exon), 49 (downstream exon)
Score: 7

TCTCACCGTGCTGCAGCGCCTCGACCACGCCGTTGAGGACATCCTCATCACCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG


Block sizes: 48 (upstream exon), 40 (downstream exon)
Score: 20

TCTCACCGTGCTGCAGCGCCTCGACCACGCCGTTGAGGACATCCTCATCACCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG


Block sizes: 39 (upstream exon), 47 (downstream exon)
Score: 5

TCTCACCGTGCTGCAGCGCCTCGACCACGCCGTTGAGGACATCCTCATCACCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG


Block sizes: 46 (upstream exon), 41 (downstream exon)
Score: 20

TCTCACCGTGCTGCAGCGCCTCGACCACGCCGTTGAGGACATCCTCATCACCGCGGCTCACGTCACGCTCTACGACTTCGACACCGACATCAACCAGTGGgtgcgttccc ... ttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacaatttggctggttggaccttatttgtgtgctcgtgttgcatgttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG
                                          atgttttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgcgttcccctgcgcgcctgtctgattcaccctgaccctgtgattcctgtgtgaacaatttggctggttggaccttatttgtgtgctcgtgttgcatgttttatgcagAGCCGGAAGGACGTGGAGGGGTCGCTCTTTGTCGTCAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG