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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttggtggctgttgatgtgatctcttttttttttttttttttggtttggcttacttaattaaaatttgtattttctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG

Basic information

species Glycine max
transcript GLYMA10G28530.2
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G28530.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0060g00600.t01 (Vitis vinifera), 3'ss of exon 8
gttggtggct-gttgatgtgatctcttttttttttttttttttggtttggcttacttaatt-aaaatttgtattttcttttta-cagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
|| ||| | |  ||||||       ||       |   | |    ||      ||||  || ||||| ||| ||   |||||  |||||| |||| ||||| ||||||||||| ||||| ||||||||||||||||||
gtgggtagtttattgatgctggtcgttgcagaagtgcatctaaaattcttggaacttgctttaaaatatgtcttccatttttgtcagCCTCTGTTTCCTGGAGAGAGTGGAGTCGATCAGCTTGTTGAGATTATCAAG

upper sequence: GLYMA10G28530.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S60_85V6.1 (Physcomitrella patens), 3'ss of exon 7
-----------------gttggtggctgttgatgtgatctcttttttttttttttttttggtttggctt--acttaattaaaatttgtattttctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
                 ||||   |  |  |   ||   | |       |    |    |  | |   |  | || |  | | | || || | ||   | |||||| ||||||| || ||||||||||| |||||| | || ||||||||||||
accacatgtgtgtgtgtgttgcaagtcggagtcatggagtttgggcgagtgaggtggaggagtagtgctgaatttgacgagattctggatgtcct---tgcagCCTCTGTTCCCCGGAGAGAGTGGAGTGGATCAATTGGTGGAGATTATCAAG

upper sequence: GLYMA10G28530.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S52_55V6.1 (Physcomitrella patens), 3'ss of exon 7
---------------------------------------------------------------------------------------------------------gttggtggctgttgatgtgatctcttttttttttttttttttggtttggcttacttaattaaaatttgtattttctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
                                                                                                         ||  |||| || ||| ||||||  || ||  |||  ||   || | ||  ||   |    | |||||  || ||     | ||||||||||||||||| || || |||||||||||| | || ||||| ||||||
gtacttatgtagttcctggtagatggtgaattcatggagattctattactcctgagtactatggttcggaatggagatagatcattgtgttgattgtaatgagatgtaagtggttggtgaagtgatca-ttgttggtttagttagatgatatgaattctgtctggacaatttcgatgttgg---tgcagCCTTTGTTCCCTGGAGAAAGCGGAGTTGATCAATTGGTGGAGATCATCAAG

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|13312851|gb|BG406502.1|BG406502
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAAC
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAAC
EST: gi|23729240|gb|BU762707.1|BU762707
EST:     GTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: GTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|19453358|gb|BM954768.1|BM954768
EST:     GTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: GTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|7926516|gb|AW832542.1|AW832542
EST:     TTGACGTCTGGTCTGTTGGATGTGTNTTAGCTGAGCTGCTTCTTGGACAG                         CCTNTGTTCCCTGGTGAGAGTGGA
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGA
EST: gi|151395928|gb|EV265805.1|EV265805
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|21677182|gb|BQ629533.1|BQ629533
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|16997089|gb|BM086461.1|BM086461
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGAT
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGAT
EST: gi|6566727|gb|AW234359.1|AW234359
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|5058458|gb|AI736869.1|AI736869
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGGAGAATATCAA
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTG-AGATTATCAA
EST: gi|27426035|gb|CA937555.1|CA937555
EST:     TCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|16104780|gb|BI892520.1|BI892520
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|151411363|gb|EV281174.1|EV281174
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|10843615|gb|BF066891.1|BF066891
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTGTGTTCCCTGGTGAGAGTGGAGTTGATCAACTAGTTGAGATTATCAAT
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|6073128|gb|AW102515.1|AW102515
EST:     TTGACGTCTGGTCTGTTGGATGTGTTNTAGCTGAGCTGCTTCTTGGACAG                         NCTTTGTTCCCTGGTGAGAGTGGAGT-GATCAACTTGTTGAGATTATCAAG
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|7926372|gb|AW832398.1|AW832398
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGAGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
EST: gi|24206278|gb|BU965531.1|BU965531
EST:     TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAG                         CCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
genomic: TTGACGTCTGGTCTGTTGGATGTGTTTTAGCTGAGCTGCTTCTTGGACAGgttggtggct ... ctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttttttttttttggtttggcttacttaattaaaatttgtattttctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG
                                   tttgtattttcttttt  CT-rich tract
                     ttacttaattaaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttggtggctgttgatgtgatctcttttttttttttttttttggtttggcttacttaattaaaatttgtattttctttttacagCCTTTGTTCCCTGGTGAGAGTGGAGTTGATCAACTTGTTGAGATTATCAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG