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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcagaagttttataactacgtttttattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC

Basic information

species Glycine max
transcript GLYMA10G07610.1
intron # 14
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os02g32610.3 (Oryza sativa), 3'ss of exon 13
gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcagaagttttataactacgtttttattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
||||||||| |||  |       ||| || || | |  |  || | ||||||      || ||    | |  ||     |||     |  |  || || |||||||||||||||| ||||| ||| | || ||||||||||| ||||||||||||||||| |||||||||||||| ||| ||||||||||    |||||||
gtaagttcatattacc-------gttacttttatttgttgattttttttcag-----cta-aatcgtgctagtaagtgctttcgatgtaatattctct-agCCTGAGTGGATGGCACCAGAAGTTATACGAGATGAGCCATCAAATGAGAAGTCTGATGTCTACAGCTTTGGTGTTATCCTATGGGAGCTCATGACATTGC

upper sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os09g39320.1 (Oryza sativa), 3'ss of exon 13
gtaagt-tcacattga--ctgcagatgttt-ctgttttgtactacttatgtttcagaagttttataactacgtttttattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
||||||  ||  |  |  || |||| |||  |  ||   | |   ||   ||  | |  || |  | ||  |  ||   |  || || | |  ||      |||||| || |||||||| || || || || || ||||| ||||| |||||||| |||||||| ||||| |||||||||||| ||||||| |||   ||| |||
gtaagtaccatttccattcttcagaagttcacccttcaatccctttttcattgaaaatattattcatctttggcttatcttgttctttttccatttaaatattagCCCGAATGGATGGCACCTGAAGTGCTCCGAGATGAACCATCCAATGAGAAATCTGATGTCTACAGTTTTGGTGTAATCCTATGGGAACTTATGACAATGC

upper sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 14
lower sequence: GRMZM2G059671_T04 (Zea mays), 3'ss of exon 12
gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcagaagttt-tataactacgtttttattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
||||||| | ||||  | | | |   | | ||||||      | |||| |  || | | | |  ||| || ||     ||| |   || |    ||   ||||||||||||||||| ||||| ||||| || || ||||| || |||||||||||||||||||||||||| |||||||||||||||||||||   |||||||
gtaagtt-atattg--ttccgtttagtgtattttgt------tttgttacgcaattctatgtggctaagtgtt-----attctgtgccatgctatc---tagCCTGAGTGGATGGCACCAGAAGTTCTACGAGACGAGCCCTCAAATGAGAAGTCTGATGTTTACAGCTTCGGTGTAATCTTATGGGAGCTTATGACATTGC

upper sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 14
lower sequence: AT5G03730.1 (Arabidopsis thaliana), 3'ss of exon 12
gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcag--aagttttataactacgtttttattaatt--tttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
|||||||||  |||  || |  |    |     || || || ||  ||||    | ||  |||  | |  |      ||| |  || ||   |||  |   | |||| ||||||||||| ||||| || || || |||||||| || ||||| ||||| ||||| |||||||| || || ||||| ||||||||||| |||||||
gtaagttcagtttgtttgaaactaaaac-acgctgaacaacgtaactttcttctaggtcctatttcca-atggaagctaaataattactgactttgatatatcagCCCGAGTGGATGGCACCAGAAGTCCTGCGAGATGAGCCGTCTAATGAAAAGTCAGATGTGTACAGCTTCGGGGTCATCTTGTGGGAGCTTGCTACATTGC

upper sequence: GLYMA10G07610.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv08s0007g03910.t01 (Vitis vinifera), 3'ss of exon 12
gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcagaagtttt-ataactacgtttt---tattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
|||||||    |   ||  | |         | |    | ||| | |||  |   | |  || | |  ||      ||| || ||| |   |||   | | | |||||||||||||||| ||||| |||||||| |||||| |||| ||||| ||||| ||  | || ||||||||| ||||||| ||||| |||||||||||||
gtaagttttactaagctagatagcaacacaatctcagttccttgtatttaggtgatatggatcattttgtcacaaatataaaatttacatttttcatttcatcagCCTGAGTGGATGGCACCAGAAGTTCTTCGGGATGAGGCATCAAATGAAAAGTCAGACATATATAGCTTTGGTATAATCTTGTGGGAACTTGCAACATTGC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttcagaagttttataactacgtttttattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC
                          tattaat  putative branch site (score: 2)
                 ctacgtttttattaat  CT-rich tract
      aagttttataactacg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagttcacattgactgcagatgtttctgttttgtactacttatgtttcagaagttttataactacgtttttattaatttttctccttttcctcccttagCCTGAGTGGATGGCTCCAGAGGTTCTTCGTGATGAGCCATCGAATGAGAAGTCTGATGTTTACAGCTTTGGTGTAATCTTATGGGAGCTTGCAACATTGC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT