Sequence
atgc intronic sequence ATGC exonic sequencegtgtttaattccaaaatccaaactcttaccttacgctagcaactattgcttcaggttgctttcttttatcaagttagttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
Basic information
species | Glycine max |
transcript | GLYMA15G09680.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g21750.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------gtgtttaattccaaaatccaaactctt--accttacgctagcaactattgcttcaggttgctttcttttatcaagttagttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
|||| | | | | ||| | || ||||| |||| | || | | || || | | | || || || ||| |||| || || ||||||| || || |||| || || || |||||||| || || |||||||||||||||||||| |||||||||||| |||| || || |
gtacactcatctattcaaacaacccctctctttctgcccttttagctttgacttatggattctgcgatctctttttagcatttatttcatcttaat-ttggggcccatgaatcatgatcataagtgataa-ctattttcagGGACTAGATACAATGGTTGGTGAGCATGGCACACAGCTATCTGGTGGACAGAAACAAAGAATTGCAATTGCAAGAGCAATTTTGAAGGACCCTAGGATAC
upper sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
lower sequence: AC233882.1_FGT003 (Zea mays), 3'ss of exon 8
gtgtttaattccaaaatccaaactcttaccttacgctagcaactattgcttcaggttgctttcttttatcaa-gttagttagtgtgttttattctgtt---tgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
||| || | | |||| | || | || ||| ||| | | | || | | || | ||| | ||| |||||||| || ||| ||| |||| |||| |||||||| |||||||||||||| ||||| || ||||| ||||| | || || || | ||| |
-------------------------gtactttcag--aaacactacttatttatgtatcttacttaagtttctgccaactaatatcttgtcttccacctcatacagGCATATGAGACAACGGTAGGTCAGCATGGTTCTCAGCTTTCTGGGGGGCAAAAGCAAAGGATTGCCATCGCAAGAGCAATCCTCAAAAATCCCAAAATTC
upper sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G46540.1 (Arabidopsis thaliana), 3'ss of exon 6
gtgtttaattccaaaatccaaactcttaccttacgctagcaactattgcttcaggttgctttcttttatcaagttagttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| |||||| | || | || | | | | |||| | || | || || ||| | || || ||| |||| | || || |||| ||| || ||||||| ||| | || |||||||||||||| || ||||| ||||| ||||| |||||||| ||||||| |||
-------------gtagtcaaactttagttataaccaagt--tggtcggtaaaacaagcttagtattct-----taattcttgt-tctttttttgtc--cagGGTTTGGAAACGATGGTAGGAGAGCATGGGACGCAATTATCCGGTGGGCAAAAGCAGAGGATTGCGATTGCGAGGGCGATTTTGAAAAACCCAAAAATAT
upper sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0003g02580.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------------------------------------------------------------gtgtttaattccaaaatc-caaactcttaccttacgctagcaactattgcttcagg-------ttgctttcttttatcaagttagttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| ||| ||| || || || || | | || | || ||| || ||||||| ||| || | | | ||||| |||| || || ||||||| || | |||| || || | ||||| || || ||||||||||||||||||||||| || ||||||||||| ||||||||||
gtgagcctatgattcattcatattcaggtcacagttgaaagagggttcaaatatacatgtctgttagaatgagtccatgaatcactgcatttcaacctcacagacctttg--taataataagagtcatgcaatcaaacaaattcttctcttcttttcatcagtattttgaatcatggtggtgtgtttacagGGGCTGGACACAATGGTGGGTGAACATGGAACGCAGTTATCTGGAGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAATCCAAGAATCC
upper sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0003g02540.t01 (Vitis vinifera), 3'ss of exon 6
------------------------------------------------gtgtttaat-tccaaaatccaaactcttaccttacgctagc-aactattgcttcaggttgctttcttttatcaagt-------tagttagtgtgttt-tattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| || | | | | | | | | ||| | | || || | || | || |||| ||| || || | || || | | ||| | |||| || || ||||||| || | |||| ||||| || ||||| || || ||||||||||||||||||||||| || ||||||||||||||| ||||||
gtaagcctattttctttctttctccttttattatggtgaaattccttcatattcagcatgctagaaaaagttacaaatcttctatttgttaaatagagaaacaattcttctttccttataaaggcctgcaatatttggaatggttgtggtgtgtatacagGGGCTAGACACAATGGTGGGTGAACATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCACGAATCC
upper sequence: GLYMA15G09680.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv10s0003g02570.t01 (Vitis vinifera), 3'ss of exon 7
-------------------------------------------------------gtgtttaattccaaaatccaaactct---taccttacg--ctagcaactattgcttcaggttgctttcttttatcaagttag--ttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
| | || || ||||| | |||| | ||| || | | ||| || | | || | | | | |||| | | | | || |||| ||||| ||||||| || || |||| ||||| || ||||| || || ||||||||||||||||||||||| || ||||||||||||||||||||||
gtgagccattctttcttaagtgaattcaaggtcatattcaggtcacagatccctgacagatctctgcagcattcaaaccataattaccgtgtagcctaataaattcttcttttccttttaatggtctaaacatctggaatggttgtggtgtgatttaattacagGGACTTGACACAATGGTGGGTGAGCATGGAACTCAGCTATCTGGGGGACAGAAGCAAAGAATTGCAATTGCAAGAGCCATTTTGAAGAACCCAAGAATCC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcaggttgctttcttttatcaagttagttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
ttttattct CT-rich tract
tttcttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgtttaattccaaaatccaaactcttaccttacgctagcaactattgcttcaggttgctttcttttatcaagttagttagtgtgttttattctgtttgtagGGCCTTGAGACAATGGCAGGCCAGAATGGGACTCAACTTTCTGGTGGGCAAAAGCAAAGAATTGCAATTGCAAGGGCAATTTTGAAGAACCCAAGAATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC