Sequence
atgc intronic sequence ATGC exonic sequence...tctgctcagaacacaaataaagttgtaatatattattcaagatcatttatttgaaggattatattggtattcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
Basic information
species | Glycine max |
transcript | GLYMA03G40600.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os01g56620.1 (Oryza sativa), 3'ss of exon 11
-------------------------tctgctcagaac-----acaaataaagttg-taatatattattcaagatcatttatttgaaggattatattggtattcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
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gtatgttatgttcaatatctgaaattttgtctagagattccaacacctgaaattaatgtaattttccttatttacgacaaatttaggctatacaattctacatattaagttgttctgattattctattcagGTATGTGCATAGTTACCAGAGTTACTTATGGAACCATGCTGCAAGTATGAGAGTTCAAAAGTATG
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G096553_T02 (Zea mays), 3'ss of exon 11
----tctgctcagaacacaaataaagttgtaatatatt-attcaagatcatttatttgaaggattatattggtattcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
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atgctctcatgttagtattcttacagttgaattttgttgaatgatggccatgtttttttt---ctatgttt-tctgaatcttttcatttgaata-ttttatgtagGTACGTACATAGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAAGTATG
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G096553_T03 (Zea mays), 3'ss of exon 11
----tctgctcagaacacaaataaagttgtaatatatt-attcaagatcatttatttgaaggattatattggtattcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
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atgctctcatgttagtattcttacagttgaattttgttgaatgatggccatgtttttttt---ctatgttt-tctgaatcttttcatttgaata-ttttatgtagGTACGTACATAGTTACCAAAGTTATCTGTGGAATCATGCTGCCAGTATGAGAGTGGAAAA-----
upper sequence: GLYMA03G40600.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv14s0030g01850.t01 (Vitis vinifera), 3'ss of exon 7
tctgctcagaacacaaataaagttgtaatatattattcaagatcatttatttgaaggattatattggta--ttcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
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-agaaatgagaggtgaatacttcttttcgactcctgtggacatgaaac-tttgtgattttagacttccaatttgaccattttattctggttctacttttcagGTATGTACATAGTTACCAAAGCTATCTGTGGAACCATGCAGCTAGTATGAGAGTGCAAAACTATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttatttgaaggattatattggtattcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
ttccactgcttttttt CT-rich tract
attatattggtattca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tctgctcagaacacaaataaagttgtaatatattattcaagatcatttatttgaaggattatattggtattcattatatagttccactgcttttttttagGTATGTTCATAGTTACCAAAGCTATTTGTGGAACCATGCTGCAAGTAAGAGGGTGCAAAAATATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
-ctgctca
- - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tccactg