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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC

Basic information

species Arabidopsis thaliana
transcript AT1G12900.2
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT1G12900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA19G28240.1 (Glycine max), 3'ss of exon 3
gttaaaacaacacttctcatatcatttgaattgaatcaacccagtt-------agatcta---aacctggtgatgatgtt-tagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC
|| || |||| || | || | | || || || | | ||| ||| | |||| ||||| | || || ||||| || || ||||||||||| |||||||| |||||||| ||||| ||||| ||| |||| || ||||| |||||||| || |||
---gtaagcctctttttcatttccatgcaactagttttactcaatttttgaagaaagtggtgtaactatgtgctattgttgcagGGACTTGGGGATAGACTTGGTGATTGAAGGAACCGGGGTGTTTGTAGACAGAGAAGGTGCAGGGAAACACATTCAAGCAGGAGCTAAGAAGGTGCTCATC

upper sequence: AT1G12900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA02G07590.1 (Glycine max), 3'ss of exon 4
-----------------------gttaaaacaacacttctca-tatcatttgaatt---gaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC-
|||| || | | ||| | || | | ||| ||| ||| | | || || | | | | ||||| | | || ||||| | || |||||||| ||||| ||||| |||||||||||||| || |||||| |||| || ||||| |||||| || | |||
aaacaaagcaacaaaacttgtcatttaactaaaaaataatcaatgtcttcttgatttctgaagcaatttgatgaaatgaaacaatattatctctttacagGGACTTGGAAATCGACTTT-TGATTGAAGGAACTGGAGTATTTGTGGACAGAGACGGTGCAGGAAAGCACATTCAAGCCGGAGCAAAGAAGATTTTGATCA

upper sequence: AT1G12900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S86_156V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------------------------------------------------gttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC
||| ||| |||| ||| | |||| ||| ||| | || | || |||| | | ||||| | | ||| || | || ||||| ||||||||||||||||| ||| | ||||||||| |||||| | |||||||||||||||||||| | |||
gtaagtacgcgttgatgactctacccccggccattcgctgtaggatctcgtactgctcaattcctgtatgtcaatgtctcatttcaacctcacatccaccgagttgaaa-aacagttcacgaatca--tgagctgacagtgctcacacgttgttg---ttgttgatactcatcagGGACATGGACATCGATCTCGTCATCGAGGGAACCGGAGTGTTTGTGGACGAGGCCGGTGCTGGCAAGCACATCCAGGCTGGAGCCAAGAAGGTATTGATC

upper sequence: AT1G12900.2 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: PP1S86_156V6.2 (Physcomitrella patens), 3'ss of exon 3
----gttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAA--CCGGAGTGTTTGTTGACAGAGACGGTGCTGGG----AAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC-------------------
|| | | | | | || | | | | | | || || | || | | || | || | | | || | || || || || | || | |||||| | | | || || | |
tctcgtcatcgagggaaccggagtgtt-tgtggacgaggccggtgctggcaagcacat-ccaggctggagccaagaaggtattgatcaccgctccaggcaagGGTCCCATCCCTACCTACGTGGTGGGAGTGAATGAGCAAGACTACAAGCACTCTGACACCATCATCAGCAACGCCTCCTGCACCACCAACTGCTTGGCAC

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|116451131|gb|EG493723.1|EG493723
EST:     TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGG---                         G-AACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGGTAAgttaaaacaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|116442534|gb|EG485126.1|EG485126
EST:     TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGG---                         G-AACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGGTAAgttaaaacaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|116408015|gb|EG450607.1|EG450607
EST:     TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCT-GGGG---                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGGTAAgttaaaacaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|116473085|gb|EG515677.1|EG515677
EST:     TCATCAAGATTGTATCTGATCGTAACCCATCTAATCCCCCCTGGGGG---                         G-AACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGGTAAgttaaaacaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|116408023|gb|EG450615.1|EG450615
EST:     TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCT-GGGG---                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGGTAAgttaaaacaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
EST: gi|116473086|gb|EG515678.1|EG515678
EST:     TCATCAAGATTGTATCTGATCGTAACCCATCTAATCCCCCCT-GGGG---                         GGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG
genomic: TCATCAAGATTGTATCTGATCGTAACCCATCTAATCTCCCCTGGGGGTAAgttaaaacaa ... tgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC
                              atctaaa  putative branch site (score: 3)
 atttgaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttaaaacaacacttctcatatcatttgaattgaatcaacccagttagatctaaacctggtgatgatgtttagGGAACTAGGCATTGACTTAGTTATCGAAGGAACCGGAGTGTTTGTTGACAGAGACGGTGCTGGGAAGCACCTTCAGGCTGGAGCCAAGAAGGTTCTTATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG