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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgaagactgcaaaccatctctatagttagttacacactgtttgatgatgctgtgacatagcttgtcctgtgcccccatgataacgataaccatctgggcgtcctgtcattatggggtcattgtacctatttcttactttgttatatgtttatgcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG

Basic information

species Zea mays
transcript GRMZM2G153977_T01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G153977_T01 (Zea mays), 3'ss of exon 4
lower sequence: LOC_Os05g49200.2 (Oryza sativa), 3'ss of exon 9
gtgaagactgcaaaccatctcta--tagttagttacacactgtttgatgat---gctgtgaca----tagcttgtcctgtgccc----ccatgataacgataaccatctgggcgtcctgtcattatggggtcattgtacctatttcttactttgttatatgtt-tatgcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG---
|| |  ||||||||   | |  |  |   |   |    |  ||  |||  |   | | ||||     ||||   |   ||| |     | ||   ||  || ||    | |   ||   |   || |   ||  |||||  | |      | |  |  ||||  |||| ||||||||  ||||||||   |||||||| |||||  |||||||| |||| ||||||   ||| | |||| ||| |||||||||||||||||||||||||| ||||||   
gtaagaactgcaaatgtttttcaagtgtctgaatctgtaaagtaggatattttcgttttgactcgattagcgattttggtgtcaagtgctatatcaattatgacttatttgagatcggattcgtaggcaatc--tgtactcactctcatttcttctccatgtggtatgtaaacacagTGCTGGAATTAAGAGCGTAGTAGATGATGAAGCTGGGGAATCGAATGGT---CTCCAAAGTGGTCCCATGTGCAATGCCTGTGAGATGGCTGTTGTATGGATG
















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|60344077|gb|DN211050.1|DN211050
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CGCTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|32795268|gb|CD947504.1|CD947504
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60400185|gb|DN232992.1|DN232992
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60339829|gb|DN206802.1|DN206802
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|21331514|gb|BQ486895.1|BQ486895
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|211224716|gb|FL222434.1|FL222434
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACAGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60352456|gb|DN219429.1|DN219429
EST:     GGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CGCTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: GGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|78120564|gb|DV538948.1|DV538948
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|31627888|gb|CD526338.1|CD526338
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|67015196|gb|CO443945.1|CO443945
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60354188|gb|DN221161.1|DN221161
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
EST: gi|60396263|gb|DN229132.1|DN229132
EST:     ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAG                         CACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG
genomic: ATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGG

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), 46 (downstream exon)
Score: 609

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1105

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1246

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 1324

ACGCAACCAGCGAAGATCTGTTCTCAGGTTGGCCTGTGCACTTTTGATGGCACTCACGGTGTTAGgtgaagactg ... gcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attatggggtcattgtacctatttcttactttgttatatgtttatgcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG
                      ttcttac  putative branch site (score: 1324)
                             tttgttatatgtttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgaagactgcaaaccatctctatagttagttacacactgtttgatgatgctgtgacatagcttgtcctgtgcccccatgataacgataaccatctgggcgtcctgtcattatggggtcattgtacctatttcttactttgttatatgtttatgcaaacacagCACTGGAATTCGTAGCGTAGTGGATGACAAAGCTGGGAAATCAAATGGTGGTCTCAAGAGTGATCCAATGTGCAATGCCTGTGAGATGGCTGTGGTATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG