Sequence
atgc intronic sequence ATGC exonic sequence...ggacacacgcgagacttggccgtaaaaattatcaatatttgatatacttttgggaaataatttttttgattttatctaaaaataattaatttgatggcagCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
Basic information
species | Glycine max |
transcript | GLYMA02G05650.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os09g35890.1 (Oryza sativa), 3'ss of exon 9
-----------------ggacacacgcgagacttggccgtaaaaattatcaatatttgatatacttttgggaaataatttttttgattttatctaaaaataatt------aatttgatggc-----agCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
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gttcacagaattctcttctgtgtctttcaaatcattctacaagt-tcatttttctctctctttcttttgaaacaagacatcttc-atttcatttaaaatgatttctgaacaacttcttggtggtgtagCAAGGGGAGAAATGGCCATATCCCATACAGAGATTCAAAGCTCACCCGGATACTGCAGTCATCACTGGGAGGCAATGCAAGAACAGCAATCATCTGCACG
upper sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g43400.4 (Oryza sativa), 3'ss of exon 8
-ggacacacgcgagacttggccgtaaaaattatcaatatttgatatacttttgggaaataatttttttgattttatctaaaaataattaatttgatggcagCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
||| || | | || ||| | | || | | || | | | |||| || || | | | |||| ||||| |||||||| ||| | || | ||||||||||||||| || || ||| | |||||||| || | ||||||||| | |||||| || ||||||||
tggatgaactaattttgaattccttttgcgcgtcgcaattcaac-tctttgattgcattattaccatccaatttagtctaagctatatgttcatgttgcagTAAGGGAAGAAATGGCCATATCCCCTACAGAGATTCAAAGCTGACTCGTATATTACAGTCTTCCTTGGGAGGCAATGCAAGAACTGCTATTATCTGCACA
upper sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G015395_T01 (Zea mays), 3'ss of exon 7
----------------------------------ggacacacgcgagactt-ggccgtaaaaattatcaatatttgatatacttttgggaaataatttttttgattttatctaaaaataattaatttgatggcagCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
||| | | | | | | || | | | | | || | || | || | | | |||| | | | | | || |||||||||| |||||||| ||| | |||| ||||||||||||||| || |||||| ||||||| || |||| ||||| || | |||||| || ||||||||
gtctgttaaggtgctctagccatctgtctttggcggataaaaccacaattccaatcatattagtgctacttttgcaatttgtcttgagccaaatgatacaacaagtgaatctggaca-actcatttctgatgcagCAAGGGAAGAAATGGGCATATCCCTTACAGAGATTCAAAGCTCACTCGCATATTGCAGTCATCTTTAGGCGGCAACGCGAGAACTGCTATTATCTGCACA
upper sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G338928_T02 (Zea mays), 3'ss of exon 4
----------------------------------------ggacaca-cgcgagacttggccgtaaaaattat-caatattt----gatatacttttgggaaataatttttttgattttatctaaaaataattaat--ttgatggcagCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
|||| | | | | || | || | |||| ||| | ||| | ||||||| || | | | | || || |||||| ||||||||| |||||||| ||| | |||| ||||||||||||||| || |||||| ||||||| || || | |||||||| | |||||| || ||||||||
gtgcgttaaggtggtctagtcatctgtctttagcagagaaaaccacaatccaaatcatattagtgttacttttgcaatttttctcgaacccccttcaacattacaatttttggacgcctaaatctagacagttcattcttgatg-cagCAAGGGAAGAAATGGGCATATCCCTTACAGAGATTCAAAGCTCACTCGCATATTGCAGTCATCTTTGGGCGGCAATGCGAGAACTGCTATTATCTGCACG
upper sequence: GLYMA02G05650.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv04s0023g03060.t01 (Vitis vinifera), 3'ss of exon 8
ggacacacgcgagacttggccgtaaaaattatcaatatttgatatacttttgggaaataatttttttgattttatctaaaaataatta---atttgatggcagCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
| | | | || | || || | | | | | | || | | || | || | | | |||||| ||||| ||||||| || |||| ||||||| |||||| ||||||||||| ||||||||||| ||||||| || |||| ||||||||| |||||||| ||||| || ||
gaatttccctttcattt---cttagtggttgtatagttgaattctgcagctgaaaggataattatcaaatctgctagttatataattgggtatttggatgcagCAAAGGAAGAAGTGGACATATTCCTTATAGAGATTCAAAATTAACCCGCATATTGCAGTCCTCCTTAGGAGGCAATGCCAAAACTGCTATCATATGTACT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.acttttgggaaataatttttttgattttatctaaaaataattaatttgatggcagCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
aaataatttttttgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggacacacgcgagacttggccgtaaaaattatcaatatttgatatacttttgggaaataatttttttgattttatctaaaaataattaatttgatggcagCAAGGGGAGAAATGGACATGTTCCTTTCAGAGATTCAAAGCTAACCCGCATACTGCAGTCTTCATTAGCAGGCAATGCTAAAACTGCAATCATCTGCACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
-gacacac
- - - - - - - - - - - - - - - - - - - - - - - cttttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaataa