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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagcctcttaattgaattcgatagtacatatacaagcatgtgaattagtaactgcatcttaaattttaataagggttctaactctcttttgaattttgaactctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCGACATGAAGAAACTGGAAGAGGCTGTTCGTGGTGTTGAGATGCCTGGTCT

Basic information

species Arabidopsis thaliana
transcript AT5G19510.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G19510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G04050.1 (Glycine max), 3'ss of exon 4
gtaagcctcttaattgaatt-cgatagtacatatacaagcatgtgaattagtaactgcatcttaaattttaataagggttctaactctcttttgaattttgaactctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCGACATGAAGAAACTGGAAGAGGCTGTTCGTGGTGTTGAGATGCCTGGTCT
         ||| ||  ||   || | |||||         |||   |   |   ||  | | ||  || | | || | |  ||    || |  ||  |||  || |||  ||||||| || |||||||| ||  | || |||||||| |||||||||||||| ||||||||||| |||||||||||||||||  |||||||||||||||||||
-------atttagttatatggtgaaattacattgttctatttgttcttcttttcttgtttttcaa--ttgagtgagtgcttaaaa---ctatcaaacattggccttttt--tagGTGGCAAATCTTCTGTTCTGCTTGACGTTAAGCCTTGGGATGATGAAACAGACATGAAGAAGCTGGAAGAGGCTGTTCGCAGTGTTGAGATGCCTGGTCT

upper sequence: AT5G19510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA14G04350.1 (Glycine max), 3'ss of exon 4
gtaagcctcttaattgaattcgatagtacatatacaagcatgtgaattagtaactgcatcttaaattttaat--aagggttctaactctcttttgaattttgaactctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCGACATGAAGAAACTGGAAGAGGCTGTTCGTGGTGTTGAGATGCCTGGTCT
         |  |||   |||   | | |  | |    | | |    |  |  ||  ||||||  || |     || |  | | || || |     | ||   ||  ||| | |||||| ||||||||||| ||  | ||||||||||| ||||| ||||| |||||||||||||| |||||||||||||| ||| || |||||||||||||| |
--------ttctatt---ttcttaatttctcacatggac-tattttcttatcgctagatcttattttcttgctgaaagcgtttgacactgtgacttaatt--gacattttat-agGTGGCAAGTCTTCTGTCCTTCTCGATGTTAAGCCTTGGGACGATGAGACCGACATGAAGAAGCTGGAAGAGGCTGTCCGTAGTATTGAGATGCCTGGTTT

upper sequence: AT5G19510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA02G44460.2 (Glycine max), 3'ss of exon 4
gtaagcctcttaattgaattcgatagtacatatacaagcatgtgaattagtaac--tgcatcttaaattttaat--aagggttctaactctcttttgaattttgaactctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCGACATGAAGAAACTGGAAGAGGCTGTTCGTGGTGTTGAGATGCCTGGTCT
              ||| ||      |||  |||        | | ||  ||||  |  ||||||  || |     || |  | | || || |    ||||    ||  ||| | |||||| ||||||||||| ||  | ||||||||||| ||||||||||| |||||||||||||| ||||||||| |||| ||  || |||||||||||||| |
-------------atgacttgtcatatactcatatggaggactaatttcttaacgctagatcttattttcttgctgaaagcatttgacactgtcactaatt---gacattttat-agGTGGCAAGTCTTCTGTCCTTCTCGATGTTAAGCCTTGGGATGATGAGACCGACATGAAGAAGCTGGAAGAGACTGTCCGCAGTATTGAGATGCCTGGTTT

upper sequence: AT5G19510.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv06s0009g02410.t01 (Vitis vinifera), 3'ss of exon 4
gtaagcctcttaattgaattcgatagtacatatacaagcatgtgaattagtaactgcatcttaaattttaataagggtt--ctaactctcttttgaattttgaactctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCGACATGAAGAAACTGGAAGAGGCTGTTCGTGGTGTTGAGATGCCTGGTCT
       |  |||| |   | | ||    ||   || |  ||    ||   ||  |  |  |  ||| | |||    ||  | |  |   |||  |||| |      | | ||||||||||| || ||||| ||  ||||||| || || ||||||||||| || ||||||||||| |||||||||||||||||  || |||||||||| || ||
-------tgataat-gtccttggtaaattatg-gcatgtttggttgttttcaatagt-ttctggattcttatagcatttgaccattttattttctaattgta-----tctattagGTGGAAAATCGTCTGTTCTTTTGGATGTGAAACCTTGGGATGATGAGACAGACATGAAGAAGCTGGAAGAGGCTGTTCGCAGTATTGAGATGCCAGGCCT

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|164101216|gb|ES090119.1|ES090119
EST:     GAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: GAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|86085215|gb|DR380974.1|DR380974
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAATGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|125242425|gb|EL256510.1|EL256510
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAG
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAG
EST: gi|125007794|gb|EL080063.1|EL080063
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGC
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGC
EST: gi|124966544|gb|EL040641.1|EL040641
EST:     ACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: ACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|125301222|gb|EL315307.1|EL315307
EST:     GAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAG
genomic: GAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAG
EST: gi|125173939|gb|EL195159.1|EL195159
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAA
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAA
EST: gi|163977579|gb|ES034425.1|ES034425
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGA
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGA
EST: gi|125300723|gb|EL314808.1|EL314808
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAA-GTCTTCTGTGCTCATGGATGTTAAGCCATGGGA
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGA
EST: gi|125092900|gb|EL150691.1|EL150691
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAG
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAG
EST: gi|164061485|gb|ES199202.1|ES199202
EST:     GGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: GGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|164020952|gb|ES013844.1|ES013844
EST:     CCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: CCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|125223374|gb|EL237459.1|EL237459
EST:     CTGCTAAGAAGGACACCCAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: CTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|125186074|gb|EL201028.1|EL201028
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTG
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTG
EST: gi|164107461|gb|ES157265.1|ES157265
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTG
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTG
EST: gi|116423792|gb|EG466384.1|EG466384
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|125006511|gb|EL078780.1|EL078780
EST:     TAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGA
genomic: TAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGA
EST: gi|164109531|gb|ES209289.1|ES209289
EST:     GTCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGG
genomic: G-CAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGG
EST: gi|125217588|gb|EL231671.1|EL231671
EST:     AGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATG
genomic: AGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATG
EST: gi|164089075|gb|ES029750.1|ES029750
EST:     CCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: CCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|125041168|gb|EL113437.1|EL113437
EST:     GCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGA
genomic: GCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGA-GAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGA
EST: gi|124709233|gb|EH800635.1|EH800635
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGG
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGG
EST: gi|125282659|gb|EL296744.1|EL296744
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAG
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAG
EST: gi|125015249|gb|EL087518.1|EL087518
EST:     AAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: AAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
EST: gi|125057778|gb|EL126826.1|EL126826
EST:     TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGT
genomic: TGCAGAGGAGAGGGAGGCTGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGT
EST: gi|124993519|gb|EL065788.1|EL065788
EST:     CAGAGGAGAGGGAGGTCTTGCTAAGAAGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGG
genomic: CAGAGGAGAGGGAGG-C-TGCTAAGAAGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGG
EST: gi|125322783|gb|EL336868.1|EL336868
EST:     AGGACACCAAGAAGCCTAAAGAGA                         GTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG
genomic: AGGACACCAAGAAGCCTAAAGAGAgtaagcctct ... tctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcttaaattttaataagggttctaactctcttttgaattttgaactctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCGACATGAAGAAACTGGAAGAGGCTGTTCGTGGTGTTGAGATGCCTGGTCT
                   ttctaac  putative branch site (score: 1)
                                            ctctttgtt  putative PPT
                              ttttgaattttgaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagcctcttaattgaattcgatagtacatatacaagcatgtgaattagtaactgcatcttaaattttaataagggttctaactctcttttgaattttgaactctttgttagGTGGAAAGTCTTCTGTGCTCATGGATGTTAAGCCATGGGATGATGAAACCGACATGAAGAAACTGGAAGAGGCTGTTCGTGGTGTTGAGATGCCTGGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGATG