Sequence
atgc intronic sequence ATGC exonic sequence...ggttgatagtctgtcaaggtctggttttgggcttgttgtataatctcctgtgtttgtgaactcatttatttcctcttttctgttgcattttccttcccagCACTCCCACTGGAGTGGAGACACCTGATGTTATTGACCTTCGTAAGCAGCAGAGGAAGGAACCTGAAAAGCCTCTTTATCAA
Basic information
species | Glycine max |
transcript | GLYMA13G25110.2 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 12
ggttgatagtctgtcaaggtctggttttgggcttgttgtataatctcctgtgtttgtgaactcatttatttcctcttttctgttgcat-tttccttcccagCACTCCCACTGGAGTGGAGACACCTGATGTTATTGACCTTCGTAAGCAGCAGAGGAAGGAACCTGAAAAGCCTCTTTATCAA------------
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------------------gtgctaccataattctttgatgccttacttagtttttctttcccaaataaagaactatgtattgatgtttgttttgctgatagCACTCCAACTGGTGTGGAAACACCTGATGTGATTGATCTTCGGAAGCTGCAGCGGAAAGAGCCTGAAAAGCAGACCGAGAAGCAACTATACCAG
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G132060_T02 (Zea mays), 3'ss of exon 11
--ggttgatagtctgtcaaggtctggtttt------gggcttgttgtataatctcctgtgtt-tgtgaactcatt---tatttcctcttttctgttgcattttccttcccagCACTCCCACTGGAGTGGAGACACCTGATGTTATTGACCTTCGTAAGCAGCAGAGGAAGGAACCTGAAAAGCCTCTTTATCAA------------
|||| | | | || | | || || | |||||| | | || | || || | || | || | | | || || | | |||| ||||| ||||| || || |||||||||||||| |||||||| |||| |||||||||||| |||| |||| | |
gtggtttactatatttctttctttagtattttgtaggtccttgttttcccttttctttagtaatgctgatgcagtagacatgtatgcctaacttttttttacctccaaccagTACTCCAACTGGTGTTGAAACACCTGATGTTATCGACCTTCGGAAGCTGCAGAGGAAGGAGACTGACAAGCAGGCAGAACGGCCGCTGTACCAG
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 7
--ggttgatagtctgtcaaggtctggttttggg----cttg--ttgtataatctcctgtgtttgtgaactcatttatttcctcttttctgttgcattttccttc--ccagCACTCCCACTGGAGTGGAGACACCTGATGTTATTGACCTTCGTAAGCAGCAGAGGAAGGAACCTGAAAAGCCTCTTTATCAA------------
| || | || | || || | |||||| |||| || | ||| || | |||| | | | | | | | | | | | |||| ||||| ||||| || || |||||||||||||| |||||||| |||| |||||||||||| |||| |||| | |
gtgatttac-gtatttctctgtattgttttgtaggcacttggttttccttttctttagtaatggtgatgcagtacacatgtagcctaattctctctctgcgtccaaccagTACTCCGACTGGTGTTGAAACACCTGATGTTATCGACCTTCGGAAGCTGCAGAGGAAGGAGACTGACAAGCAGGCAGAACGGCCGTTGTATCAG
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 12
lower sequence: AT4G21660.2 (Arabidopsis thaliana), 3'ss of exon 12
-ggttgatagt-ctgtcaaggtctg-gttttgggcttgttgtataatctcctgtgtttgtgaactcatttatttcctcttttctgttgcattttccttcccagCACTCCCACTGGAGTGGAGACACCTGATGTTATTGACCTTCGTAAGCAGCAGAGGAAGGAACCTGAAAAGCCTCTTTATCAA
||| || | | | | || | | | || || | | | | | | | | | || | | || ||| || | | ||||||||| ||||| | |||||||| |||| ||||| ||||||||| | ||||| ||||||||||| | | |||| || ||
gtattgttatcattatgcatttatgaggtgtatactatttatttgtttccttatcagtataatctaagtataaagctgatttgtgattttccccttctttcagCACTCCTACTGGTATAGAGACACCGGATGCAATTGAACTTCGTAAGGATCAGAGAAAGGAACCTGATAGGGCTCTATACCAG
upper sequence: GLYMA13G25110.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv00s0818g00010.t01 (Vitis vinifera), 3'ss of exon 4
ggttgatagtctgtcaaggtctggttttgggcttgttgtataatctcctgtg---tttgtgaactcatttatttcctcttttctgttgcattttccttcccagCACTCCCACTGGAGTGGAGACACCTGATGTTATTGACCTTCGTAAGCAGCAGAGGAAGGAACCTGAAAAGCCTCTTTATCAA
|| | || | | | | ||| || ||| || | | |||| | || ||| | || || | || | | || | |||||| || ||||| || ||||||||||||||||||||||| |||||||| ||||||||||| || || | ||| |||||||||
--gggaccattagtaaggagtctgggcaagtctttctgcatatcatcttaagaaacttgtaatctttattaatga-tcactttttttccctcctcttattcagCACCCCAACTGGTGTTGAGACACCTGATGTTATTGACCTACGTAAGCAACAGAGGAAGGAGCCAGAGAGGCCACTTTATCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcctgtgtttgtgaactcatttatttcctcttttctgttgcattttccttcccagCACTCCCACTGGAGTGGAGACACCTGATGTTATTGACCTTCGTAAGCAGCAGAGGAAGGAACCTGAAAAGCCTCTTTATCAA
ctcatttatttcctct CT-rich tract
tcatttattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggttgatagtctgtcaaggtctggttttgggcttgttgtataatctcctgtgtttgtgaactcatttatttcctcttttctgttgcattttccttcccagCACTCCCACTGGAGTGGAGACACCTGATGTTATTGACCTTCGTAAGCAGCAGAGGAAGGAACCTGAAAAGCCTCTTTATCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA