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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtttggttcctctctttcttgggtgtcatcacatctttgcatggatgactgaatgctgcccttgtggtttctgagcggacctgatgttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCCATCAGGGGTTTGTACTATGACAGACTTAAAGGGTGCCTACTCAAGCTTG

Basic information

species Zea mays
transcript GRMZM2G040945_T01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G040945_T01 (Zea mays), 3'ss of exon 3
lower sequence: LOC_Os09g25640.1 (Oryza sativa), 3'ss of exon 3
gtttggttcctctctttcttgggtgtcatcacatctttgca--tggatgactgaatgctgcccttgtggtttctgagcggacctgatgttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCCATCAGGGGTTTGTACTATGACAGACTTAAAGGGTGCCTACTCAAGCTTG
||||| ||  ||      || |  |    |    |||| ||      ||  ||| |   ||  |||||| || |||||||  |||||||||| |||||||||||||||||||||| |||||| |||| |||||||||| |  ||| |||||||||||  | || ||||||||| | ||||| |||||  | |||||||
gtttgattgttcgtggctttagtggcttactggcctttccagtcttctgcatgagtcacgctgttgtgggttgtgagcgg--ctgatgttttgtgcagTTGAAGTATCCGGAGAGCTGCTTGAAGTATGAGTATGACCACGGCTTTCCCATCAGGGGGCTCTATTATGACAGATTAAAAGGTTGCCTTTTGAAGCTTG
















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|71771543|gb|DR969480.1|DR969480
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|76020827|gb|DT947997.1|DT947997
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|76020213|gb|DT947383.1|DT947383
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|211377248|gb|FL413757.1|FL413757
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCAC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCAC
EST: gi|148971904|gb|EE022679.2|EE022679
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|76915905|gb|DV166160.1|DV166160
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|148935914|gb|EC879965.2|EC879965
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|76925058|gb|DV170275.1|DV170275
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|211082071|gb|FL392683.1|FL392683
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|93283038|gb|EB675302.1|EB675302
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|78103885|gb|DV522308.1|DV522308
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|71417284|gb|DR803998.1|DR803998
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|94475337|gb|EB704295.1|EB704295
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
EST: gi|78111525|gb|DV529922.1|DV529922
EST:     ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAG                         TTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC
genomic: ACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCC

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: 139

CCAGGTCTACGGCTTCGACTACGACTACACGCTGTCGCACTACTCCGAGCACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCCATCAGGGGTTTGTACTATGACAGACTTAAAGGGTGCCTACTCAAGCTTG


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 17

CCAGGTCTACGGCTTCGACTACGACTACACGCTGTCGCACTACTCCGAGCACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCCATCAGGGGTTTGTACTATGACAGACTTAAAGGGTGCCTACTCAAGCTTG


Block sizes: 48 (upstream exon), 39 (downstream exon)
Score: 16

CCAGGTCTACGGCTTCGACTACGACTACACGCTGTCGCACTACTCCGAGCACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCCATCAGGGGTTTGTACTATGACAGACTTAAAGGGTGCCTACTCAAGCTTG


Block sizes: 44 (upstream exon), 48 (downstream exon)
Score: 20

CCAGGTCTACGGCTTCGACTACGACTACACGCTGTCGCACTACTCCGAGCACCTGCAATGCCTTATCTACGATCTTGCCAAAAGGCACTTGGTCAATGAGgtttggttcc ... ttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCCATCAGGGGTTTGTACTATGACAGACTTAAAGGGTGCCTACTCAAGCTTG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggatgactgaatgctgcccttgtggtttctgagcggacctgatgttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCCATCAGGGGTTTGTACTATGACAGACTTAAAGGGTGCCTACTCAAGCTTG
                                     acctgat  putative branch site (score: 20)
                                           tgttttct  CT-rich tract
                                          atgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtttggttcctctctttcttgggtgtcatcacatctttgcatggatgactgaatgctgcccttgtggtttctgagcggacctgatgttttctgcagTTGAAGTATCCGGAGAGTTGCTTGCAGTACGAGTATGACCGCACCTTCCCCATCAGGGGTTTGTACTATGACAGACTTAAAGGGTGCCTACTCAAGCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT