Sequence
atgc intronic sequence ATGC exonic sequencegtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
Basic information
species | Glycine max |
transcript | GLYMA02G44000.3 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g57680.1 (Oryza sativa), 3'ss of exon 4
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
| | ||| | | || | || | | ||| || | | ||| || | | ||| | | || | ||| | ||| | ||| ||| ||||| || |||||||||||||||||||||||||| | ||| | ||| | || || ||||| || || || | || | || |||
-----------------------------------------------------------------ggtgctaagaatgaaaggagcaaccaagattattatagttgagagttcctaacaat---tttaggagaaatacttacacccaatttctatt--------tttttgttacagGTGAAACTTGAATCCCAATACTATTTCTACATGGAGACACAGACGGCCTTAGCTATCCCTGATGAAGATAACTGTATAACCCTCTATGTGTCGGCGCAAC
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g04860.1 (Oryza sativa), 3'ss of exon 4
---------------gtacatgtaacatatccattgtttcctccttctactcctttcac-atctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtt--tctgaat--aatgaattttga----tgagaatatattgat-caagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
| | ||||| | ||| | | ||| || | | | | | || | | || | | || | || || ||| ||||||| || ||| | | | || || || | || | | | ||| | | | | || | || ||| ||| |||||| || || |||||||||||||||||||||||| | || | ||| | || || ||||| || || || || ||| ||| ||||
gtacggacatttcgttttctcttaacacgctaaagctttaattttgctattctatatattaattagaagaacaattttgattcacactggaatctactgagcaacagagttgctctgaatgaaacgaaatatatagcctcagttcatgacaattctaggagaaataccttcaccttatttgttttttg--ggcacatacagGTGAAACTTGGATCCCAGTACTATTTCTACATGGAGACACAAACGGCTTTAGCTTTCCCTGATGAAGATAACTGTATAACCGTCTACTGCTCAGCGCAAA
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G141473_T01 (Zea mays), 3'ss of exon 4
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
||| | | ||| |||||| ||| | | || | |||| | | | | | | | | || | | ||||| | |||| ||||| ||||| | | ||||| || |||||||||||||||||||||||||||| || || ||| | || || ||||| || || || | || ||| | ||||
------------------------------------------------------------gtacat-actttgtgatgtttaaaggaagagcactctttaa--aggaatgt-----acacttgacttccccacaatgccaaacaac-tcatgcttggaatttt-tgtttc-tgcagGTAAAACTTGAATCCCAATACTATTTCTACATGGAGACACAAGTGGCGCTAGCTATTCCTGATGAAGATAACTGTATAACCATCTATTCTTCGACACAAA
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
lower sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtt-taatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
| | || | | | | | ||| ||| | || | || | || | | | | || ||| | || |||| | || | | | | |||||||||| ||||||||| || |||| ||||| |||||||||||| | || ||||| | || || |||||||| || | |||||||||| ||||| ||||
------------------------------------------------------------------------gtattaaaat-tctctttctctctcttaatctttgatat--attaaaaaaaaataaaaaaaaatacattcttacactatgtttgctgttgattttggttatgcagTTGAGACTTGGGTCACAGTACTTCTTCTATATGGAGACACAAACAGCACTTGCCTTGCCAGATGAAGACAACTGTTTAGTGGTTTACAGTTCAACTCAAG
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02410.t01 (Vitis vinifera), 3'ss of exon 4
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
| ||| |||| || | || || ||| || ||| | ||||| ||| | | ||| | | || || | | | |||| || || ||| | | ||||||||| || || |||||||| |||||||||||| |||||||||| || ||||| |||||||| |||||||||||||||| ||||| |||
------------------------------------------------------gtacttctcattta-cttgttatacaattttt---ttctattcctattaatgtttttc--------tttcttgttttggt---tttatgataaatgctttctgaatt----gtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAGTTCCCGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02430.t01 (Vitis vinifera), 3'ss of exon 4
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
| ||| |||| || | || || ||| || ||| | ||||| ||| | | || | | || || | | | |||| || || ||| | | ||||||||| || || |||||||| |||||||||||| |||||||||| | || || |||||||| |||||||||||||||| ||||| ||
------------------------------------------------------gtacttctcattta-cttgttatacaattttt--tttctattcctattaatgtttttc--------tttcctgttttggt---tttatgataaatgctttctgaatt----gtcacatccagATCAGACTTGGGTCACAGTATTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCGGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAGT
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv18s0041g02390.t01 (Vitis vinifera), 3'ss of exon 3
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
||||| | | | || | | || ||| || || || ||||| | | | | | | || || | | | | ||||| || || ||| | | ||||||||| ||||| || ||||| |||||||| ||| |||||||||| || || || ||||| || |||||||||||||||| | ||| |||
------------------------------------------------------------gtacttc--tcatttacttgttatgcaatttttttcctatttatattatttttttcc---tttctctttttggt---tttatgataaatactttctaaatt----gtcacatccagATCAAACTTGGGTCACAATATTACTTCTATATGGAGACCCAAACTGCCCTTGCAGTTCCAGATGAAGATAACTGCATTGTGGTTTACAGTGCAATACAAT
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 4
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 4
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
|| | | |||| || | || | ||| | ||||| | || || ||| | | | | ||| | || | | | | | |||| | | ||| | | ||||||||| || ||||||||||| |||||||||||| |||||||||| | || || |||||||| |||||||||||||||| ||||| |||
------------------------------------------------------gtatttgtcattta-cttgttatacaaattttgttcctatttct-attagtgtttttctttta---ttttttggt--------tttgtgatgaataattgctgaatt-gtcctcatgtccagATCAAACTTGGGTCACAGTACTATTTCTATATGGAGACACAAACTGCCCTTGCAATTCCAGATGAAGACAACTGCATTGTGGTTTACAGTTCAATACAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
aaattcaatgtttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatgtaacatatccattgtttcctccttctactcctttcacatctttgtggccatctctactttagtttctgatgtgatgtttaagtttgtttctgaataatgaattttgatgagaatatattgatcaagcatattcattgtcatcatgtatcaaattcaatgtttaatgcagTTGACACTTGGGTCTCAATACTATTTCTACATGGAGACACAAGCTGCCCTTGCTGTACCCGACGAAGACAATTGCATTGTGGTTTACATTTCAAGTCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA