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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggattcaaaacttattggtggttcaccattttgttgagtattttatttctctctttttttgcgtgatacaagacgttgtggaaccatttaccattgttaactcttcacttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTATCCACTATGTTGCAAAATAGTTGAAGTGCTGCATAAGTCCCAGCTACAAT

Basic information

species Zea mays
transcript GRMZM2G144362_T06
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G144362_T02 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os06g41390.4 (Oryza sativa), 3'ss of exon 5
gttggattcaaaacttattggtggttcaccattttgttgagtattttatttctctctttttttgcgtgatacaagacgttgtggaaccatttaccattgttaactcttcacttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTATCCACTATGTTGCAAAATAGTTGAAGTGCTGCATAAGTCCCAGCTACAAT
|||| |||  | |          |   ||  | | ||| |     ||  ||   | ||| || || ||||||       | | | | ||| ||   |  |  | | | |||  |   ||||||| | |||  |||||| ||| ||||||||||||||||||||||||||||||||||||||||  ||| |||| ||| || ||||||||| ||  ||||
gttgaatttcaga----------gcgtactgtgtggttaaac---ttcctttaatttttgttagcatgatac------ctataggatcatgtaatttactatattttgcaccgc---agGTTGTACATTCTGCTGGAAGGAAGCACATCAAACAGGAAGGGTATTCCTATCCACTATGTTGCAGGATACTTGAGGTGTTGTATAAGTCCCGGCAGCAAT
















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|76291844|gb|DV031412.1|DV031412
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|94474973|gb|EB703931.1|EB703931
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCGTGGAAAGAAA
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTC-TGGAAAGAAA
EST: gi|76286746|gb|DV026314.1|DV026314
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|71441108|gb|DR822158.1|DR822158
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|78088519|gb|DV516912.1|DV516912
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|78079635|gb|DV508047.1|DV508047
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|148933496|gb|EC877205.2|EC877205
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|91055958|gb|EB166376.1|EB166376
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|89249445|gb|DY621231.1|DY621231
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|148985933|gb|EE029846.2|EE029846
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGCTCCTCTGGAAACAAACACATCAAACAGGAAGGGTATTCCTA
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTA
EST: gi|149014216|gb|EE043770.2|EE043770
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|71430541|gb|DR811591.1|DR811591
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|93282998|gb|EB675262.1|EB675262
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|76937601|gb|DV175194.1|DV175194
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|93281830|gb|EB674094.1|EB674094
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|71332805|gb|DR803405.1|DR803405
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|50333623|gb|CO528749.1|CO528749
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|78123131|gb|DV541515.1|DV541515
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAGG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|94477309|gb|EB706267.1|EB706267
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|76010683|gb|DT937853.1|DT937853
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
EST: gi|71449941|gb|DR830991.1|DR830991
EST:     GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAG                         GTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT
genomic: GTTCACCTTATTGGTGGCTTTGCTGATGCTTCCACAAAGgttggattca ... acttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cgtgatacaagacgttgtggaaccatttaccattgttaactcttcacttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTATCCACTATGTTGCAAAATAGTTGAAGTGCTGCATAAGTCCCAGCTACAAT
                                 tgttaac  putative branch site (score: 2)
                                       ctcttcacttcttc  CT-rich tract
                               attgttaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggattcaaaacttattggtggttcaccattttgttgagtattttatttctctctttttttgcgtgatacaagacgttgtggaaccatttaccattgttaactcttcacttcttcagGTTGTTCGTTCCTCTGGAAAGAAACACATCAAACAGGAAGGGTATTCCTATCCACTATGTTGCAAAATAGTTGAAGTGCTGCATAAGTCCCAGCTACAAT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC