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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtctctctccctccctctctctctttctcttttctaaacattaatttttaatattggcttccctggattcagatcatcatttttgtttatttgaccttgtaattgactttcattccagGATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTTCTTGATGAAGCTGATGAAATGTTGAGGATGGGATTTGTTGAGGATGTTG

Basic information

species Arabidopsis thaliana
transcript AT5G62190.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G62190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GRMZM2G149520_T02 (Zea mays), 3'ss of exon 3
gtacgtctctctccctccctctctctctttctcttttctaaacattaatttttaatattggcttccctggattcagatcatcatttttgtttatttgaccttgtaattgactttcattccagGATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTTCTTGATGAAGCTGATGAAATGTTGAGGATGGGATTTGTTGAGGATGTTG
                                    | |     |||  |||  || |     ||  || || ||  |  |||||| ||    |||     | |  |  |       | ||||||   ||||  | |  ||  ||  |||| |  |  ||  |||||||||| ||||||||||||||||| ||| | |  ||||| |||||||| ||||| |
-----------------------------------gtgtttgtcttatctttgcatctccagctcattgcat-catgtgctcatttctgcagttttttatgtatgctacatcacttgtgcagGATTTCATTGTTAAAGGAACTCTCAATTTGAAATGCTTGAAATTCCGTGTCCTTGATGAAGCTGATGAGATGCTAAACATGGGTTTTGTTGATGATGTCG

upper sequence: AT5G62190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: GLYMA10G38680.1 (Glycine max), 3'ss of exon 3
-------------------------------------gtacgtctctctccctccctctctctctttctcttttctaaa--------cattaatttttaatattggcttccctggattcaga--tcatcatttttgtttatttgaccttgtaattgactttcattccagGATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTTCTTGATGAAGCTGATGAAATGTTGAGGATGGGATTTGTTGAGGATGTTG
                                      ||  |   | || |    | |   | |   |  || | |||        ||  ||   ||    |||  |    |  |  || |  |   || | || | |  ||  | |  |   ||  | |   |  ||||||||||||| |    |||  ||||  | ||| |  || | || ||||| ||||||||||| ||||||||| |||||||||| |||||||| |||||||
gtaattgcagtaacactagttgatcgattatacgaagctagtttgttatctccttatatgaatgtaaattattgcaaaagtagattgcacgaaagcttggctttgtgtgttttaaagacaaaagttgacaatattttgtgatttccatcttggatg--tattggtgtagGATCATATTGAGAAGGGAAATATTGACCTGAGCCAACTAAAGTTTCGTGTCCTTGATGAAGCCGATGAAATGCTGAGGATGGGTTTTGTTGAAGATGTTG

upper sequence: AT5G62190.1 (Arabidopsis thaliana), 3'ss of exon 3
lower sequence: Vv16s0022g02110.t01 (Vitis vinifera), 3'ss of exon 3
gtacgtctctctccctccctctctctctttctctt-ttctaaacattaattttta-----atattggcttccctggattcagatcatcatttttgtttatttgaccttgtaattgactttcattccagGATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTTCTTGATGAAGCTGATGAAATGTTGAGGATGGGATTTGTTGAGGATGTTG
|||| |   |||   ||  | ||  |||  | | | ||||||   |  |  ||||     || |    ||    |  ||| |     ||||  || | ||       |  ||   | |    ||  ||||||| || || ||   |||  |||| ||||||| |||| | |||||||| |||||||| ||||||||||||||||||||||| |||||||| |||||||
gtactttcttctttttcaatttcattctagcccctgttctaattttgcagatttatttgcatgtaaaatttttagtgttctgtatcccattcatgctaatactgatgtccaagcaaatcatgttgtagGATCACATAGAGAGGGGAAATATTGACTTCAGCTCTTTAAAGTTCCGTGTCCTTGATGAGGCTGATGAAATGTTGAGGATGGGTTTTGTTGAAGATGTTG

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|124973901|gb|EL047497.1|EL047497
EST:     AATTAAAGAGAGGTGTTGACATTGTAGTTGGAACCCCTGGTCGTATTAAG                         GATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTT
genomic: AATTAAAGAGAGGTGTTGACATTGTAGTTGGAACCCCTGGTCGTATTAAGgtacgtctct ... ttcattccagGATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTT
EST: gi|47828150|gb|CK117834.1|CK117834
EST:     AATTAAAGAGAGGTGTTGACATTGTAGTTGGAACCCCTGGTCGTATTAAG                         GATCATATTGAAAGACAAAACCTTGATTTCAGCTATCTACAATTCCGTGTT
genomic: AATTAAAGAGAGGTGTTGACATTGTAGTTGGAACCCCTGGTCGTATTAAGgtacgtctct ... ttcattccagGATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tggattcagatcatcatttttgtttatttgaccttgtaattgactttcattccagGATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTTCTTGATGAAGCTGATGAAATGTTGAGGATGGGATTTGTTGAGGATGTTG
                                     aattgac  putative branch site (score: 3)
                                           ctttcattcc  CT-rich tract
            atcatttttgtttatt  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
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---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacgtctctctccctccctctctctctttctcttttctaaacattaatttttaatattggcttccctggattcagatcatcatttttgtttatttgaccttgtaattgactttcattccagGATCATATTGAAAGACAAAACCTTGATTTCAGCTATTTACAATTCCGTGTTCTTGATGAAGCTGATGAAATGTTGAGGATGGGATTTGTTGAGGATGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGATG