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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgccgtccctggttcttgattgttgacctgcatgctttgcttcctttttacattccaatacataccagttccctccattaagttcttgtttccaaggtcgcttaaacatggtcgttttatgctgacttttgttttatactacagCATAAAACCATTGATGGTGTCCTAGCCCGAGGTGAAAAGCTGGACAGCTTAGTGGAGAAGAGCTCAGAGTTAAGCCTGGCATCGAAG

Basic information

species Arabidopsis thaliana
transcript AT5G58180.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA13G19950.1 (Glycine max), 3'ss of exon 4
gtaagtgccgtccctggttcttgattgttgacctgcatgctttgcttcctttttacattccaatacataccagttccctccattaagttcttgtttccaaggtcgcttaaacatggtcgttttatgctgacttttgttttatactacagCATAAAACCATTGATGGTGTCCTAGCCCGAGGTGAAAAGCTGGACAGCTTAGTGGAGAAGAGCTCAGAGTTAAGCCTGGCATCGAAG
                                       ||||| |   || || |    |||||        ||   | |  ||  ||  || |    || || |||        ||   ||||| || ||||   ||||||  |||||||||||| |||||| |||| || ||  |||| || ||||||||||| ||||| |||||||| || ||  | ||    |||||| ||
---------------------------------------ctttgttcatttcttcctgcacaataggc-ttgtttaggttctctagttttctggtgtgtagatctctt--------tcaccttatgatgtctttctgtttataa-acagCATAAAACTATTGATAGTGTGCTGGCTAGAGGGGAGAAGCTGGACAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCATCGCAG

upper sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: GLYMA09G13840.1 (Glycine max), 3'ss of exon 4
gtaagtgccgtccctggttcttgattgttgacctgcatgctttgcttcctttttacattccaatacataccagttccctccattaagttct-tgtttccaaggtcgcttaaacatggtcgttttatgctgacttttgttttatactacagCATAAAACCATTGATGGTGTCCTAGCCCGAGGTGAAAAGCTGGACAGCTTAGTGGAGAAGAGCTCAGAGTTAAGCCTGGCATCGAAG
                                                 ||| | |||| |     | || | ||  ||   ||| ||||| || ||    |||   |  |   |  ||   ||||| || ||||   ||||||  |||||||||||| |||||| |||| |||||  |||| || |||||||| || ||||| |||||||| || ||  | ||    || ||| ||
------------------------------------------------ttttgttcatttcttcctacac-aattggcttgtttaggttctctggttttctggtgtgtagatttttttcaccttatgatgtctttctgtttataa-acagCATAAAACTATTGATAGTGTGCTAGCTAGAGGGGAGAAGCTGGATAGTTTAGTTGAGAAGAGTTCTGATCTGAGTGCCGCTTCGCAG

upper sequence: AT5G58180.1 (Arabidopsis thaliana), 3'ss of exon 4
lower sequence: Vv11s0206g00130.t01 (Vitis vinifera), 3'ss of exon 4
gtaagtgccgtccctggttcttgattgttgacctgcatgctttgcttcctttttacattccaatacataccagttccctccattaagttcttgtttccaaggtcgcttaaacatggtcgttttatgctgacttttgttttatactacagCATAAAACCATTGATGGTGTCCTAGCCCGAGGTGAAAAGCTGGACAGCTTAGTGGAGAAGAGCTCAGAGTTAAGCCTGGCATCGAAG
                                         | |    || | | |  || |||         ||   ||| |    || || |||           |  |     |  ||| ||    | |||| | || |   ||||||||| || |||||| ||||||| || |||||||| ||||||||||| ||||| ||||| || |||||  | |||   |||||  ||
-----------------------------------------tggagaactatctgctgtctaattttgtttccttttttccttc---tttttattttt----ctatctttattcttttctttgatatgtatttttctgtt-tgacacagCATAAGACTATTGATAGTGTCCTTGCACGAGGTGAGAAGCTGGACAGTTTAGTTGAGAAAAGTTCAGATCTCAGCACAGCATCACAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccaaggtcgcttaaacatggtcgttttatgctgacttttgttttatactacagCATAAAACCATTGATGGTGTCCTAGCCCGAGGTGAAAAGCTGGACAGCTTAGTGGAGAAGAGCTCAGAGTTAAGCCTGGCATCGAAG
                              tgctgac  putative branch site (score: 2)
                                    cttttgtttt  CT-rich tract
                                     ttttgttttatacta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtgccgtccctggttcttgattgttgacctgcatgctttgcttcctttttacattccaatacataccagttccctccattaagttcttgtttccaaggtcgcttaaacatggtcgttttatgctgacttttgttttatactacagCATAAAACCATTGATGGTGTCCTAGCCCGAGGTGAAAAGCTGGACAGCTTAGTGGAGAAGAGCTCAGAGTTAAGCCTGGCATCGAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTCA