Sequence
atgc intronic sequence ATGC exonic sequencegtgtgttgctttgaaagtctaacattactaatatcaattcatgtgcaactacaattagatatcctcatttactgtggtgacacttttgtttttattgttttgcatccataagGCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAG
Basic information
species | Glycine max |
transcript | GLYMA12G36520.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 16
lower sequence: LOC_Os01g67740.1 (Oryza sativa), 3'ss of exon 15
gtgtgttgctttgaaagtctaacattactaatatcaattcatgtgcaactacaattagatatcctcatttactgtggtgacacttttgtttttattgttttgcatccataagGCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAG
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--------------------------gtacatat-gattc-tgaatagcttcaattggttaatctg---caatttcatcaagcacaaattatcaataactttcacatgca-gTCTTGAGAAGAGGGTCAATAAGAAAGTTATGGCAATGTTTGAGAAGGCAGAGGATGAGTATAATGATTTGATGTCAAAGAAAAACATCATTGAG
upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 16
lower sequence: GRMZM2G006452_T02 (Zea mays), 3'ss of exon 9
---------------------------------------------------------------------gtgtgttgctttgaa-agtctaacattactaatatcaattcatgtgca-actacaattagatatcctcatttactgtggtgacacttttgtttttattgttttgcatccataagGCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAG
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gtacatttgatatttctattggctccataattgataaaccatcataattactcctgacattttttgaatatatgatgatttggacaggttgctagtgctactgaattgctgtatccatatcacctcccaattctgtaatttgcaatgtattcacca--atctttattacct-gtttgca---gTCTTGAGAAGAGGGTCAATAAGAAAGTAATGGCAATGTTTGAGAAGGCGGAGGATGAGTACAATGATTTGATGTCAAAGAAAAACATCATCGAG
upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 16
lower sequence: AT5G62410.1 (Arabidopsis thaliana), 3'ss of exon 15
----gtgtgttgctttgaaagtctaacattactaatatcaat-tcatgt---------gcaactacaattagatatcctcatttactgtggtgacacttttgtttttattgttt--tgcatccataagGCTTG-AGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAG
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gtatgtgtatgagaattaacgttttatctttatgaaacctatattatattgtcgtcacatcattgaagtgaaatatcaatatgacatgcattcttcttcttttcctggttatttatttccctcatgaagCTTGGAAAAAAGAGTGAACAAGAAGGTTATGGCTATGTTTGAGAAAGCAGAAGATGAATACAATGCTCTGATATCGAAAAAAAATACTATCGAG
upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 16
lower sequence: AT3G47460.1 (Arabidopsis thaliana), 3'ss of exon 15
------------------------------------------------gtgtgttgctttgaaagtctaacattactaatat-caattcatgtgcaactacaattagatatcctcatttac-tgtggtgacacttttgt--ttttattgttttgcatcc----ataagGCTT-GAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAG
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gtatgtttctaaggatagtcatagatttaattttgcaacttatataatattcactctcatgcaa-tgcaatatcaatggaatgtgctttatttttcttttttgtttcttctctttaattaaatgagaaatctctcctctcgtttcctggctattcattctcttataaagTCTAGAGAAAAGAGTGAACAAGAAGGTCACGGCTATGTTTGAGAAAGCTGAAGATGAATATAATGCTCTTATGACCAAGAAAAATATAATCGAG
upper sequence: GLYMA12G36520.1 (Glycine max), 3'ss of exon 16
lower sequence: Vv16s0022g00060.t01 (Vitis vinifera), 3'ss of exon 15
gtgtgttgctttgaaagtctaacattactaatatcaattcatgtgcaactacaat-tagatatcctcatttactgtggtgacacttttgtttttattgttttgcatccataagGCTTG-AGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAG
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--------actcaaacgtagtaccgtgctatcattatcttctgtgaaatgaagaggtagcaaagaacaattttt-tactga-----ttgttttttcttcttttcactaatgtagCCTGGAGAAAAGGGTGAATAAGAAAGTTATGGCAATGTTTGAGAAAGCAGAAGATGAGTACAATGAATTAATATCCAAGAAAAGCATAATTGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatatcctcatttactgtggtgacacttttgtttttattgttttgcatccataagGCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAG
ttttgtttttattgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtgttgctttgaaagtctaacattactaatatcaattcatgtgcaactacaattagatatcctcatttactgtggtgacacttttgtttttattgttttgcatccataagGCTTGAGAAAAGGGTGAACAAGAAAGTGATGGCAATGTTTGAGAAGGCTGAAGATGAGTACAATGATTTGATGTCCAAAAAAAACATAATTGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG