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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attatacctcatgattcgcaaattttgctttaccatttattttgttacgattgtacattggaggctcggatcaatatcttttgacattttttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG

Basic information

species Zea mays
transcript GRMZM2G307906_T01
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G307906_T01 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os03g15700.1 (Oryza sativa), 3'ss of exon 3
attat----acctcatgattcgcaaattttgctttaccatttattttgttacgattgtacattggaggctcggatcaatatcttttgacattttttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG
||| |    |  |  || ||   ||||||  | |||  |   |||     | |  | ||  || |      ||    ||| ||||||| |||| |   |||||||||||||| || ||||| ||||| ||  ||||||||||||||||||||||| ||||||||||||||
attttgaggatattttgtttttaaaatttatccttataac--attagaacatgtatataattttgtacgctggggtgataacttttgatatttctc--ttttagATTGGTTATCCTGAAATTGAAGAAAACAGCAAGCCAAGGCACCGTTTCATGGCATCATATGAACAG
















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|76290809|gb|DV030377.1|DV030377
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211458274|gb|FL247609.1|FL247609
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211458279|gb|FL247614.1|FL247614
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211458288|gb|FL247623.1|FL247623
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211458277|gb|FL247612.1|FL247612
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGG
EST: gi|211294858|gb|FL410176.1|FL410176
EST:     ATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: ATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211298410|gb|FL370609.1|FL370609
EST:     GATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: GATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|78117919|gb|DV536306.1|DV536306
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCCAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|5268368|gb|AI770332.1|AI770332
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211397249|gb|FL247600.1|FL247600
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211458281|gb|FL247616.1|FL247616
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGAT
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGAT
EST: gi|78091778|gb|DV520152.1|DV520152
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211397251|gb|FL247602.1|FL247602
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|74241998|gb|DT649912.1|DT649912
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211397255|gb|FL247606.1|FL247606
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|74236877|gb|DT644791.1|DT644791
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211458286|gb|FL247621.1|FL247621
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211460798|gb|FL247624.1|FL247624
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211397254|gb|FL247605.1|FL247605
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211397257|gb|FL247608.1|FL247608
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         ATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCCAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
EST: gi|211458275|gb|FL247610.1|FL247610
EST:     TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAA                         AYTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG
genomic: TAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATG

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: 47 (upstream exon), 48 (downstream exon)
Score: 105

TTAAGATTGGCAGACCTGGGTATAAAGTAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG


Block sizes: 49 (upstream exon), 40 (downstream exon)
Score: 73

TTAAGATTGGCAGACCTGGGTATAAAGTAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 143

TTAAGATTGGCAGACCTGGGTATAAAGTAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG


Block sizes: 46 (upstream exon), 48 (downstream exon)
Score: 69

TTAAGATTGGCAGACCTGGGTATAAAGTAACCAAACAATATGATCCTGAGATGAAGCAACACTCGTTTCTTTTTGAAgttagtattc ... ttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgattgtacattggaggctcggatcaatatcttttgacattttttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG
                                 ttttgac  putative branch site (score: 69)
                                       cattttttcatttt  CT-rich tract
                           aatatcttttgacatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attatacctcatgattcgcaaattttgctttaccatttattttgttacgattgtacattggaggctcggatcaatatcttttgacattttttcattttagATTGGTTACCCGGAAATCGAAGATAATTGCAAGCCAAGGCACCGTTTCATGTCATCATATGAACAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - -catgatt
- - - - - - - - - - - ttttgct
- - - - - - - - - - - - - - - - - - - -ttttgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - tggaggc