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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagattttggtgactgcctacttttcagtcttcatcaatcactgtttgctaatccttttcttccttctccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAAAGTTGATTCTGGTGGTTACACATCATTGGATGATGTCACAAGCCTACCT

Basic information

species Zea mays
transcript GRMZM2G150201_T03
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GRMZM2G150201_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os05g11850.1 (Oryza sativa), 3'ss of exon 5
---------------------------------------------------------------------------gtaagattttggtgactgcctacttttcagtctt-catcaat--cactgtttgctaatccttt----tcttccttctccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAAAGTTGATTCTGGTGGTTACACATCATTGGATGATGTCACAAGCCTACCT
                                                                            || |   |     || |||        || |   ||  |||  |||   |  |||  | |||    ||| | ||        ||||||||||||| |||||||||||||| |||||||||||||||||||| |||| ||||||||||||||| || || ||||||||||||||||||||| | || 
gtaagatataacactactttattatctttaggtcacctgccactcaattttgaataatgttatgggttagggttcatagggggtaaac-accgccgggaggatagccaggcaataatgccaccactgactatccttttattatctccttttcttttacacagGTATAGGGAATGGGGTTGGCAGATTTTTCAGGCTTTTGAGAAGTATACAAGAGTTGATTCTGGTGGCTATACTTCATTGGATGATGTCACAAGCTTGCCC

upper sequence: GRMZM2G150201_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA15G10130.1 (Glycine max), 3'ss of exon 5
------------------------------------------------------------------------------------gtaagattttggtgactgcctacttttcagtcttcatcaatcactgtttgctaatccttttcttccttctccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAAAGTTGATTCTGGTGGTTACACATCATTGGATGATGTCACAAGCCTACCT
                                                                                     |||  || |  |  |||     |||| |    || |   |  || |    |||||   |       | |   |  |||| ||| | || ||||||||||| |||||| | |||||||| ||| ||||||| |||||| ||||||| ||    ||  |||| ||||| || |   | |||
gtatgctttctccctttcttatgtataaaattagtttatatttctattgcttctggccatgtgtaagaaacagtgaaaacaagcttaattttgtttttcctgttctttttttaaaaatcttttttttctttgaaataatcagatatgaatattttgtcttacagATATCGTGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAAGCACACAAAGGTTGATACTGGTGGATATTGTTCTCTGGACGATGTAACTATTGTTCCT

upper sequence: GRMZM2G150201_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA13G28910.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------gtaagattt--tggtgactgcctacttttcagtcttcatcaatcactgtt-----tgctaatccttttcttccttctccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAAAGTTGATTCTGGTGGTTACACATCATTGGATGATGTCACAAGCCTACCT
                                                             ||||||     ||   ||   ||   |||   | ||| | | ||  | ||     |  |||||   |       | |      |||| ||| |||| ||||||||||| |||||| | |||||||| ||  ||||||| |||||| ||||||| ||    ||  |||| ||||| || ||  | |||
gtatgcttttacccttcttatgtataagattagtttatacttctatttcttctggccatgtgtaagaaacagtgaaaacaagcttaattttgtttttcctgattcttttttctttgtaataatcagatatgaatattttgtgttacagATATCGGGAATGGGGTTGGCAAATCTTTGAAGCTTTTGAAAATCACACAAAGGTTGATACTGGTGGATATTGTTCTCTGGACGATGTAACTAGTGTTCCT

upper sequence: GRMZM2G150201_T03 (Zea mays), 3'ss of exon 5
lower sequence: AT1G30000.1 (Arabidopsis thaliana), 3'ss of exon 5
---------gtaagattttggtgactgcctact--tttcagtcttcatcaatcactgtttgctaatccttttcttccttctccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAAAGTTGATTCTGGTGGTTACACATCATTGGATGATGTCACAAGCCTACCT
          ||    |  | |     |  |||  | | |||  |     |  | | |   || |    |  |    ||||  |    ||| ||  | ||    |||||||| || ||| | |||||||| ||||||||||| ||  | || ||||| |||||||||||||||||||| |||    | |||
gtatgaaaactattcatccgattttccctcactaatctaagttcttggggactattctactcttaaagctaacacatttctaaaattgcagATACCGAGATCAAGGTTGGCAAATTTTTGAAGCTTTTGAAAAGTACACAAAGGTGAAATCAGGTGGATACACATCATTGGATGATGTAACAGAAGTGCCT

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|60397080|gb|DN229899.1|DN229899
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|5915252|gb|AW052893.1|AW052893
EST:     AGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: AGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|14204264|gb|BG837941.1|BG837941
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|78022171|gb|DV490558.1|DV490558
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|211200407|gb|FL096660.1|FL096660
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAA-TACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|33102054|gb|CF062014.1|CF062014
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|71761675|gb|DR959612.1|DR959612
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|5770177|gb|AI973351.1|AI973351
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|5325061|gb|AI783252.1|AI783252
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|32833265|gb|CD972943.1|CD972943
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTA
EST: gi|74233685|gb|DT641599.1|DT641599
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|6563800|gb|AW231332.1|AW231332
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|5846873|gb|AI999956.1|AI999956
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
EST: gi|101393290|gb|EB818576.1|EB818576
EST:     GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAA                         GTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA
genomic: GAGACTGTGGAATCACTATTTGTTTTGTATAGAATCACAGAGGATTCCAAgtaagatttt ... ccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcagtcttcatcaatcactgtttgctaatccttttcttccttctccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAAAGTTGATTCTGGTGGTTACACATCATTGGATGATGTCACAAGCCTACCT
                       tgctaat  putative branch site (score: 2)
                  ctgtttgctaatcctt  CT-rich tract
                                ttttctt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagattttggtgactgcctacttttcagtcttcatcaatcactgtttgctaatccttttcttccttctccacgaacagGTATAGGGAGTGGGGTTGGCAGATCTTTCAGGCTTTTGAGAAGTACACAAAAGTTGATTCTGGTGGTTACACATCATTGGATGATGTCACAAGCCTACCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG