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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcccctatgtgcacatgtttgcttccctagtaatgggacccttctaatttatatactgacgttcctattcttcatttctttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG

Basic information

species Zea mays
transcript GRMZM2G082664_T01
intron # 17
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G082664_T01 (Zea mays), 3'ss of exon 17
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 20
----gtcccctatgtgcacatgtttg----cttccctagtaatgggacccttctaatttata--tactga-cgttcctattcttc---------atttctttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG
     | | || | |   | |  ||     ||        | |  ||     |||| || |   || ||| | ||  |||   ||           |  | |||  |||||||| ||||| || || |||||||| ||||||||||||||||| || || |   ||||||
gtactttctctctcttttcctaattaaggactcgaacgaaactaagattacactaagttgtcattattgagcttttgtatctctctggtttaatgctgttatcttgcagTCTGGTATTCTTGCTGTTGGTAGAGGCAACAAGGTTGTTGAACCAGTGGTTGGAGGCGATG
















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|71433813|gb|DR814863.1|DR814863
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGTATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|61119124|gb|DN560085.1|DN560085
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|211174833|gb|FL413958.1|FL413958
EST:     TTGGGATGTACMCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|76924990|gb|DV170231.1|DV170231
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|8930105|gb|BE224943.1|BE224943
EST:     ACCCTGTGGACCATTTCTGTGCAATCATTAATCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: ACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|60347222|gb|DN214195.1|DN214195
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCG
EST: gi|149003161|gb|EE038899.2|EE038899
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|60337715|gb|DN204688.1|DN204688
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|47961688|gb|CN844397.1|CN844397
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|50331519|gb|CO526645.1|CO526645
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|37398003|gb|CF636310.1|CF636310
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|148945040|gb|EC890224.2|EC890224
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|40337298|gb|CK371368.1|CK371368
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|50331482|gb|CO526608.1|CO526608
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|50331518|gb|CO526644.1|CO526644
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTTTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|50331481|gb|CO526607.1|CO526607
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|91053971|gb|EB164389.1|EB164389
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
EST: gi|88758153|gb|DY542294.1|DY542294
EST:     TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAG                         TCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG
genomic: TTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTG

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), 46 (downstream exon)
Score: 131

TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG


Block sizes: 48 (upstream exon), 49 (downstream exon)
Score: 118

TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG


Block sizes: 49 (upstream exon), 49 (downstream exon)
Score: 131

TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG


Block sizes: 47 (upstream exon), 49 (downstream exon)
Score: 108

TATCTCGAATCTTGGGATGTACCCTGTGGACCATTTCTGTGCAATCATTAACCCTCCACAGgtcccctatg ... tttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG




 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgggacccttctaatttatatactgacgttcctattcttcatttctttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG
                    tactgac  putative branch site (score: 108)
                          cgttcctattcttcat  CT-rich tract
        ttctaatttatatact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcccctatgtgcacatgtttgcttccctagtaatgggacccttctaatttatatactgacgttcctattcttcatttctttctatcagTCTGGCATTCTCGCAGTGGGTAGAGGAAACAAGGTTGTTGAACCTGTTGTGGACAGCGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA