Sequence
atgc intronic sequence ATGC exonic sequence...ttaaatgtaaactagttgtaagtggggggaggtcttgcagattcagaacttgctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA
Basic information
species | Glycine max |
transcript | GLYMA18G47600.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G868168_T01 (Zea mays), 3'ss of exon 3
ttaaatgtaaactagttgtaagtggggggaggtcttgcagatt-cagaacttgctaaatctt-tttgctgtt-ttttctttcttctttttgacataat---gaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-
|| || | | | | ||| | || || ||| || | | |||| ||| || | ||| | || ||| | | ||||| | ||||||||||| ||||| |||||||| || || ||||| || ||||| || | |||||| |||| || || || ||||||||||||||
-------actacgcattctgttcactgttatattttgatgttttcatgactcagtaggtttggtttgttgtagttatgattcaaaataatgttatacttttgtgtagATTAGACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
upper sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G868168_T03 (Zea mays), 3'ss of exon 3
ttaaatgtaaactagttgtaagtggggggaggtcttgcagattcagaacttgctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-
|| | | ||| | | || || || || |||| | | | | || | | | ||| | | || || | || ||||| | ||||||||||| ||||| |||||||| || || ||||| || ||||| || | |||||| |||| || || || ||||||||||||||
--gcat-tctgttcactgtta-tattttgatgttttcatgactcagtaggt-ttggtttgttgtagttatgattcaaaataatgttatacttt-tgtgtagattagACATGGTGAAGCAGTTGGGATAATTGGACCTTCAGGGACGGGAAAATCAACTATATTGAAGGTTATGGCTGGGCTGCTTGCTCCGGACAAG
upper sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G65410.1 (Arabidopsis thaliana), 3'ss of exon 2
ttaaatgtaaactagttgtaagtg--gggggaggtcttgcagattcagaa---cttgctaaatctttttgct--gttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-
|| | ||| |||| | || | ||| ||||| ||| | | || | | | | |||| | | | |||| | ||||||||||||||||| | |||||||| ||||| ||||| ||||| ||| |||| |||||||| || || ||||||||||| |||||
--gtattttgttgtgtttacagtgatgaaagaaggcttatagattttgaaaggcacacaaagacaccacacaaagacaccacattctaaccaatttttaagtatgcagATTAGACATGGTGAAGCTGTTGGGGTGATTGGTCCTTCTGGAACTGGAAAATCAACAATTTTAAAGATTATGGCTGGTCTTCTTGCTCCAGACAAG
upper sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0023g00290.t01 (Vitis vinifera), 3'ss of exon 2
ttaaatgtaaactagttgtaagtggggggaggtcttgcagattcagaactt--gctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-
| || | | |||| | | | | | ||| || | || | || | | | | || || | | || | || |||||| | ||||| ||||||||||| || ||||| || ||||| ||||| ||||| |||||| ||||||||||||| |||||||||||||| |||||
--gagtg-gatttttttgtctctcttttcatatttagtttcccttgaattttggttatgttttatcattctctgtttattttcttactttaacccatttatagATTAGACATGGGGAAGCTGTTGGGATTATTGGGCCTTCTGGCACTGGGAAATCAACAGTTCTGAAGATTATTGCGGGACTTCTTGCTCCAGACAAG
upper sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S18_59V6.1 (Physcomitrella patens), 3'ss of exon 4
-ttaaatgtaaactagt-tgtaagtggggggaggtcttgcagattcagaacttgctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-
|||| || | |||| || || ||||| || | || | || | | | ||| ||| | | | || | | | |||| |||||||| || ||||| || |||||||||||||| || ||||||||||| || | || || || |||||||||||||| || ||
cttaactgcccattagtgtggaaagctcgggagttccagtgtgcacata-tatgaggattggcgtggct--tttcaatatgcttattccaatgtgcttgtcagATACGACATGGTGAGGCAGTTGGCATCATTGGTCCCTCTGGCACAGGCAAATCTACTATTCTCCGCATCATGGCTGGACTTCTTGCTCCAGATAAG
upper sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ22908 (Selaginella moellendorffii), 3'ss of exon 1
ttaaatgtaaactagttgtaagtggggggaggtcttgcagattcagaacttgctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-
|| |||| || | ||| | | || | | | ||||||||| || || |||||||| ||||| ||||| ||||| || ||||| || || || || || ||||||||||||| || |||||||||| ||| |||||
----------------------------------gtgtggatt--gagcagcataacgactgtcactctctaaatccttttctttttgt--------gcagGTCCGCCATGGTGAGGCTGTGGGAATTATTGGACCTTCTGGAACAGGAAAGTCCACGATTTTGAAGATTATGGCTGGACTTCTTGTTCCTGACAAG
upper sequence: GLYMA18G47600.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ30431 (Selaginella moellendorffii), 3'ss of exon 1
ttaaatgtaaactagttgtaagtggggggaggtcttgcagattcagaacttgctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA-
|| |||| || | || || | || | | | ||||||||| || || |||||||| ||||| ||||| ||||| || ||||| || || || || || ||||||||||||| || |||||||||| ||| |||||
----------------------------------gtgtggatt--gagcagcatagcgattgtcactctctaaatccttttctttttgt--------gcagGTCCGCCATGGTGAGGCTGTGGGAATTATTGGACCTTCTGGAACAGGAAAGTCCACGATTTTGAAGATTATGGCTGGACTTCTTGTTCCTGACAAGMapped 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|13480728|gb|BG510071.1|BG510071EST: GTGTACAAGTCTTTTGGGGAAAAGAAAATCTTAAATGGTGTCAGCTTCAA GATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAA
genomic: GTGTACAAGTCTTTTGGGGAAAAGAAAATCTTAAATGGTGTCAGCTTCAAggtaaggatt ... ataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAA
EST:
gi|17023590|gb|BM094624.1|BM094624EST: GTGTACAAGTCTTTTGGGGAAAAGAAAATCTTAAATGGTGTCAGCTTCAA GATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAA
genomic: GTGTACAAGTCTTTTGGGGAAAAGAAAATCTTAAATGGTGTCAGCTTCAAggtaaggatt ... ataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaacttgctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA
tctttttgctgttttt CT-rich tract
taaatcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttaaatgtaaactagttgtaagtggggggaggtcttgcagattcagaacttgctaaatctttttgctgttttttctttcttctttttgacataatgaataGATCAAGCATGGTGAAGCTGTTGGAATAATTGGTCCCTCTGGGACTGGCAAATCTACAGTTTTGAAGATTATTGCAGGACTTCTTGCTCCGGACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - tgggggg
- - - - - - - - - - - - - - - - tcttgca