Sequence
atgc intronic sequence ATGC exonic sequencegtaaaaacctgcaacattatgcctactcatttatttattttattttttgtttttttgttttctcaatccgctttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA
Basic information
species | Glycine max |
transcript | GLYMA08G20900.1 |
intron # | 15 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 15
lower sequence: LOC_Os01g36930.1 (Oryza sativa), 3'ss of exon 15
----------------------------------------------------------------------------------------------------------gtaaaaacctgcaa-cattatgcctactcatttatttattttattttttgtttttttgttttctcaatccgctttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA
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gcaagtagttggcttctgttcttatttagagaaatagctcagatacttgtactctttgtttgtcaaatggtggggtttttctgcctcttattatgttagggttctagtgtatctattcaagtagcatgctgcgacccatactt-caatactttcaatctggttagctttatgcttagctgtgttgtgtgtttactgcagCCGATTCTTCTGTGCCAAAGAAACATT--TGACTGGCATCTATGATTTAATTGCTGTTTTGACGCACAAAGGGAGAAGTGCAGACTCAGGCCATTATGTTGG---------
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G017086_T03 (Zea mays), 3'ss of exon 15
----gtaaaaacctgcaacattatgcct--actcatttatt-tattttattttttgtttttttgttttctcaatccgcttt--ctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA
|| | ||| | | || | || | | || | | | | || | || | |||| || ||| | ||| || |||| | | || |||||| | ||||| | ||||||||||||||||| || || |||||||| |||||||| || || || || ||||||||
gaaagtttgaccctctacctgtaaggctgtaatgatcgaggacactgctagtgttatcttactagcttctaaacttagtttgctcatgtgttaaatgcagCTGAGTCT-TCTCTACCAAAGAAACA--ATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG---------
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 15
lower sequence: GRMZM2G028733_T01 (Zea mays), 3'ss of exon 15
-----------------------------------------------------gtaaaaacctgcaacattatgcctactcatttatttattttattttttgtttttttgttttctcaatccgctttctgct--ttttactccattctctgtctatagGTGA---------AAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA
| | | || | ||| | || | ||| | ||||| ||| | | |||| | | || ||| ||| | | | || ||| | | | ||| | ||||| | ||||||||||||||||| || || |||||||| |||||||| || || || || ||||||||
gcaagttgtttgtttctgccctcattttgtaatgatacaccttattgtcaaacttcatttcttgggattatattcttaggacccaaaaagtttcaccctttgtctttgatgatacgcaatacaatatccaaaaggtttgctc-gtgtgttaaatgcagCTGAGTCTTCTCTACCAAAGAAACAATTAACTGGCGTCTATGATTTGGTTGCTGTCTTGACACACAAGGGAAGAAGTGCAGACTCTGGCCACTATGTTGG---------
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 15
lower sequence: AT1G51710.1 (Arabidopsis thaliana), 3'ss of exon 14
---------------------------------------------------------------------gtaaaaacctgcaacattat--gcctactcatttattt-atttta--------------ttttttgtttttttgttttctcaatccgctttctgctttttactccattctct---gt-ctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA
||||| || | | ||| | | ||| || || | |||| | || | | || | | | ||||| | | || | | | | || || ||| |||||||| || ||||||||||| ||||| ||||| ||||| || |||||||||||||| ||||| || || || ||||||||||
gtacattatctaagacccccttttcaacatttttcttttctggcttggaaagagcggtaattggtttgtgtaaatactttgatgattgtttgtctatctatagatctcatttcaaagcaatcaagaaccttgtcagagcctaattgtgaggaatctaattctgttatataatggaactttttagGTACTTCTTCTGAGAAGGAAACTCACATGACTGGAATCTATGACTTGGTCGCTGTGTTGACCCACAAGGGCAGGAGTGCAGACTCTGGTCATTATGTTGC---------
upper sequence: GLYMA08G20900.1 (Glycine max), 3'ss of exon 15
lower sequence: Vv09s0002g02500.t01 (Vitis vinifera), 3'ss of exon 15
--gtaaaaacctgcaacattatgcctact----catttatttattttattttttgtttttttgttttct-caatccgctttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA
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atgtaatgtgcttatgtcgaatcccttctatgacagtgctgcactatgcctatggaacgtctctcttttgcagtttggttgctaactttgtttactgcagGCGTTC-CAACCGACAAGGAAACACACTTGACTGGAATTTATGATCTGGTTGCTGTGTTGACCCACAAGGGCAGGAGTGCTGATTCAGGGCATTATGTTGC---------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|13789583|gb|BG652174.1|BG652174EST: GGATCATTGAATGGAGGGGAGCCATCTGTAGTTCCCATGGAGGAGG GTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAA
genomic: GGATCATTGAATGGAGGGGAGCCATCTGTAGTTCCCATGGAGGAGGgtaaaaacct ... ctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAA
EST:
gi|17022113|gb|BM093147.1|BM093147EST: GGATCATTGAATGGAGGGGAGCCATCTGTAGTTCCCATGGAGGAGG GTGAAAAGGAAACACAGATGACTGGAATTTATGAT
genomic: GGATCATTGAATGGAGGGGAGCCATCTGTAGTTCCCATGGAGGAGGgtaaaaacct ... ctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttttttgttttctcaatccgctttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA
tccgctttctgctttt CT-rich tract
tttgtttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaaacctgcaacattatgcctactcatttatttattttattttttgtttttttgttttctcaatccgctttctgctttttactccattctctgtctatagGTGAAAAGGAAACACAGATGACTGGAATTTATGATTTGGTTGCTGTATTAACCCACAAGGGCAGAAGTGCTGATTCAGGACATTATGTTGGTTGGGTCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT