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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ggcttttgtgtagatgtgctaacagttgtttattgcagcctcttacattgttgttaattttatggattgatttgcttactttgttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG

Basic information

species Glycine max
transcript GLYMA16G25400.1
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g12710.1 (Oryza sativa), 3'ss of exon 5
ggcttttgtgtagatgtgctaacagttgtttattgcagcctcttacattgttgttaatttta-tggattgatttgcttacttt--gttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
 ||| || |  |  | || |||  |||   | |  |  ||  ||  ||      | |||  |   |||  |||    |         |   |  ||    |||| ||||||||||||||||||| ||||||||  ||||| ||||||||||| ||||| || ||||  |  |||
agctctttt-cacttctgttaa--gttcactttaactccccgttttatcagccatgattgcagcagatcaattaatctgtagaaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTGACATCGTATTTAACTTCAACAAG

upper sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g25110.1 (Oryza sativa), 3'ss of exon 4
ggcttttgtgtagatgtgctaacagttgtttattgcagcctcttacatt-gttgttaattttatggattgatttgcttactttg-ttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
 ||        |       ||| | | | |  |  |   |  ||  ||  |   | | |      |||  |||    |        |   |  ||    |||| ||||||||||||||||||| ||||||||  ||||| ||||||||| | || || || ||||  |  |||
-gcacagcctcaaggacagtaaaaat-gctcttaactctccattttatcagccatgattgcggcagatcaattaatctgtagaaactttatcttgtgcacagTTTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTGTGTGAGCTTCACATTGTATTTAACTTCAACAAG

upper sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177914_T05 (Zea mays), 3'ss of exon 4
ggcttttgtgtagatgtgctaacagttgtttat-tgcagcctcttacattgttgttaattttatggattgatttgcttactttgttcctttct-gccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG-----------------------------
      ||   |  | |  |  |     ||| | |  |    ||||    | | |   | |    |||||||     ||   |     | ||| |    |||||||||||||||||||||||| ||||||||  |||||||| |||||||| ||||| || ||||  |  |||                             
-ataactgaagacttattttgtcttccttttgtctaaaaggacttat-cagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAGGTACCATATGTCCATATGATCCTACTTTT

upper sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G177914_T03 (Zea mays), 3'ss of exon 4
ggcttttgtgtagatgtgctaacagttgtttat-tgcagcctcttacattgttgttaattttatggattgatttgcttactttgttcctttct-gccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
      ||   |  | |  |  |     ||| | |  |    ||||    | | |   | |    |||||||     ||   |     | ||| |    |||||||||||||||||||||||| ||||||||  |||||||| |||||||| ||||| || ||||  |  |||
-ataactgaagacttattttgtcttccttttgtctaaaaggacttat-cagctctggttctaggagattgatcactctatactaactttgtctcgtgcacagTGTTTGTTGAAACATTGGACAGATGCTTCAAGAATGTATGCGAGCTTGACATCGTATTTAACTTCAACAAG

upper sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G50860.1 (Arabidopsis thaliana), 3'ss of exon 4
-ggcttttgtgtagatgtgctaacagttgtttattgc--agcctcttacattgttgttaattttatggattgatttgcttactttgttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
    || | | |   | ||||   |  |  || ||||  | |   ||  |    | ||    || |    ||||||    | || ||| ||| |      ||||  ||||||||||| |||||||||||||||| ||||| || || || || || ||||||||||| || |||
atcattgtctattcctctgctcgtaaattctttttgcttaacgctttgaaaatgtattctcattgtatgatgattta--aagttagtttcttgc-attggcagTTCTTGTTGAAACACTGGACAAATGCTTCAGCAATGTCTGCGAACTCGACATTGTGTTCAACTACAGCAAG

upper sequence: GLYMA16G25400.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0023g01770.t01 (Vitis vinifera), 3'ss of exon 4
-ggcttttgtgtagatgtgctaacagttgtt-tattgcagcctcttacattgttgttaattttatggattgatttgcttactttgttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
 |  | |  | |  || |   |  || |    ||   |||    ||  ||  ||||||||    |    | ||||| ||||| |   |  |||||||||||||  | || |||||||||||||| ||||||| ||||||||| |||||||| || |||||||| ||||| |||
agcatatcatcttcatatcaaataagctaaaatacaacagtgcttttgatatttgttaat--ggtcatatcatttgtttactcttgactcttctgccttcagTTCTGGTGGAAACATTGGACAAGTGCTTCAAAAATGTATGCGAGCTTGACATAGTGTTCAATTATAGCAAG

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|192308409|gb|FK002809.1|FK002809
EST:     CATATTTGATAGTTCTGAAAACGAGCTTGCTATGCTTGACTTGATACAAG                         TGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATA
genomic: CATATTTGATAGTTCTGAAAACGAGCTTGCTATGCTTGACTTGATACAAGgtagattatg ... ctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATA
EST: gi|213600159|gb|DB979780.1|DB979780
EST:     CATATTTGATAGTTCTGAAAACGAGCTTGCTATGCTTGACTTGATACAAG                         TGTTTGTTGAAACAAAAGACAAATGCTTCAGAAATGTATGTGAGCTTGATA
genomic: CATATTTGATAGTTCTGAAAACGAGCTTGCTATGCTTGACTTGATACAAGgtagattatg ... ctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cattgttgttaattttatggattgatttgcttactttgttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG
                           tgcttac  putative branch site (score: 2)
                         tttgcttactttgttc  CT-rich tract
        ttaattttatggatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ggcttttgtgtagatgtgctaacagttgtttattgcagcctcttacattgttgttaattttatggattgatttgcttactttgttcctttctgccttcagTGTTTGTTGAAACATTGGACAAATGCTTCAGAAATGTATGTGAGCTTGATATCGTGTTCAACTATAGTAAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT