Sequence
atgc intronic sequence ATGC exonic sequencegtatgatttggttgccatttgtttgaatttaacttcattgaatttattttttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
Basic information
species | Glycine max |
transcript | GLYMA07G35010.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g30020.1 (Oryza sativa), 3'ss of exon 5
gtatgatttggttgccatttgtttgaatttaacttcattgaatttattttttt-taaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||||| | | | | || || ||| ||| | || | | | | | ||||| | | | | || | | ||||||| | || ||||| |||||||| || ||||| ||||||||||| |||||||| || || | ||||| || || | ||||||||||||||||| |||
gtatgctattgataccctta--------ttatctttagagatatcactcaatcatgtatataacacgttaaaaag-ggcgtatattgtacagGCTGCGTACTTCGCTTTGCCTGCAGTTCAAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: AC233979.1_FGT009 (Zea mays), 3'ss of exon 4
gtatgatttggttgccatttgtttgaatttaacttcattg----aatttattttttttaaatatatttgttcac-acac-tggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
| || | |||| |||| | || | | | ||| || | || || || | | |||| || | |||||| | || || || |||||||||||||| || || ||||||||||| ||||| || ||||| ||||| ||||| | ||||| |||||||||||||||
----------------gtatgctaaaattactcttcctcattacaaatagtaatccacaaacatccctatttactacgccttaaaaggggtgtacagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGTGCAATCTTCCTCGCTGCGAAGTTTCTCAAAGTCAAGCTTCCATCAGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G308570_T02 (Zea mays), 3'ss of exon 13
gtatgatttggttgccatttgtttgaatttaacttcattg----aatttattttttttaaatatatttgttcac-acac-tggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
| || | |||| |||||| || | | | ||| || | | || | || | |||| || | |||||| | || || || |||||||||||||| || || ||||||||||| || || || ||||| ||||| ||||| | ||||| |||||||||||||||
----------------gtatgctaaaattactcttcatcactgcaaatagtaatccacaaacatgcctacttactataccttaaaaggggtgtgcagGCTCCGCACTTCACTTTGCCTGCAATTTAAACCGCACCATATTGCGGCTGGCGCAATCTTCCTGGCTGCGAAGTTTCTTAAAGTCAAGCTTCCATCAGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G115670_T01 (Zea mays), 3'ss of exon 4
gtatgatttggttgccatttgtttgaatttaacttcattgaatttattttttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||||| | | | || || | | || || |||| | || || | || || | | | || | || | ||| ||| | || ||||| ||||||||||| |||| ||||||||||| |||||||| || || | ||||| || || | ||||||||||||||||| |||
gtatgctagtgctacccttactgtcgtttgaa----attgcagttcacagttgtgtatctactacacttaatattgtgcactg---tacagACTGCGTACTTCGCTTTGCCTGCAATTCGAGCCTCATCATATTGCAGCAGGTGCTATCTTTTTGGCTGCTAAATTTCTCAAAGTGAAGCTTCCATCTGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G45190.1 (Arabidopsis thaliana), 3'ss of exon 5
gtatgatttggttgccatttgtttgaatttaacttcattgaatttattttttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||| | || | |||| || | | || | | | ||| | || || | | |||| ||| || |||||||||| ||| || ||||||| |||||||||||||||||||| |||||||||||||| ||||| || || ||||| ||||||||| | ||||||||| | |||||||||
gtacg-ttcaagaactatttccttctaaa-gcttccaataattctatgtgccttgtattttcgtcttcatacaatgaaaagtggcttgcagTCTACGGACATCTCTCTGCCTGCAATTTAAGCCTCATCATATTGCGGCTGGTGCAATATTTCTTGCGGCCAAGTTCCTTAAAGTGAAGTTACCATCAGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: AT4G19600.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatgatttggttgccatttgtttgaatttaacttcat-tgaatttattttttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||| | || | ||| ||||| | ||||| | || ||| | | || || | || |||| ||| || |||| |||| ||| ||| |||| || |||||||||||||||||||| || || |||||||| || || ||||| |||||||| |||||| | |||||||| | |||||||||
gtacg-ttaaaagtctgtttccttgaa---agcttcagatagatctatctgtcttgtattttcttcttcatacaatgaaaagatgcttgcagTCTGCGGACGTCACTCTGCCTGCAATTTAAGCCTCACCACATTGCGGCGGGAGCAATTTTTCTTGCTGCGAAGTTCCTTAAAGTGAAATTACCATCAGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv00s0125g00270.t01 (Vitis vinifera), 3'ss of exon 4
gtatgatttggttgccatttg------------tttga--atttaacttcattgaatttatttt----ttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
|||||||| | ||| ||| ||||| || | |||| | | | || | || | || ||||||||||||||| ||||| ||||||||||||||| |||||||||||||||||||| | || ||||| ||||||||||||||||||||||||||||| | ||||||||||||||||| |||
gtatgattaagatgctttttcatgtctctcttttttgatagttccatttcaaatggtctctcttcctctctttctcttcttcactcacacactggaaagcggcttgcagGCTGAGGACATCACTCTGCCTGCAATTTAAGCCCGACCACATTGCAGCAGGTGCCATTTTCCTTGCTGCCAAGTTTCTCAAAGTGAAGCTTCCATCGGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S264_33V6.3 (Physcomitrella patens), 3'ss of exon 5
------gtatgatttggttgccat-ttgtttgaatttaacttcattgaatttattttttttaaat-atatttgttcacacactggaaagtggcttt-cagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
| || | || || || | | || | ||| | | | || || | | | | | | | || || || || | | ||| || | |||||| | ||||||||||| ||||| ||||||||||| || || || || ||| | ||||||||||| ||||||||||| || || ||||
ttagagatttgccaggtaagctatattacagaagaacatgtttaatgagcatgtctgttgcaagtgagaatagctgaggcaaggggaaagggttgtgcagTCTTCGCACATCGTTGTGCCTGCAATTCAAGCCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAGTTTTTGAAAGTGAATCTGCCCAAAGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S119_132V6.1 (Physcomitrella patens), 3'ss of exon 4
--------gtatgatttggttgccatttgtttgaatttaactt---cattgaatttattttttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
| | ||| | | | ||| | ||| | | || | | | | || || | || | | | || || || | | ||| || | || ||||| || ||||||||||| || ||||||||||| || || || || ||| | |||||||||||| | |||||||| || || ||||
tccatagagatttgccaggtaagcctatttttcagaagaacatgtgtaatgtacatgtctgttgcaagtgaatg-gctgaggcaa-ggggagggttgtgcagCCTTCGCACCTCGCTATGTCTGCAATTTAAACCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAGTTCCTTAAAGTGAACCTCCCCAAAGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ37217 (Selaginella moellendorffii), 3'ss of exon 4
------------------gtatga--tttggttgccatttgtttgaatttaacttcattgaatttattttttttaaatatatttgt-tcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||| || || || | | | | || || | | | | ||| | ||| | | || | | | || ||||| | | | |||||| | ||||||||||||||||| || |||||||| || || || || |||||||||||||| ||||| ||||| | || |||||||| || |||
gtaagctctcgcacaccagtaggaacttcagtctcgactggagtg--ttggagtccgtgttgtttcatcactttgatgagatgggaatgaagcagtggaagg-gatgtgcagGCTACGCACATCGCTCTGCCTGCAGTTCAAGCCACACCACATCGCCGCCGGTGCCATTTTCCTGGCTGCAAAGTTTCTTAAGGTGAAGCTGCCGATCGAT
upper sequence: GLYMA07G35010.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ27727 (Selaginella moellendorffii), 3'ss of exon 4
------------------gtatga--tttggttgccatttgtttgaatttaacttcattgaatttattttttttaaatatatttgt-tcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
||| || || || | | | | || || | | | | ||| | ||| | | || | | | || ||||| | | | |||||| | ||||||||||||||||| || ||||| || || || || || |||||||||||||| ||||| ||||| | || |||||||| || |||
gtaagctctcgcacaccagtaggaacttcagtctcgactggagtg--ttggagtccgtgttgtttcatcactttgatgagatgggaatgaagcagtggaagg-gatgtgcagGCTACGCACATCGCTCTGCCTGCAGTTCAAGCCGCACCACATCGCCGCTGGTGCCATTTTCCTGGCTGCAAAGTTTCTTAAGGTGAAGCTGCCGATCGAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgaatttattttttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
ctttc CT-rich tract
atttattttttttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgatttggttgccatttgtttgaatttaacttcattgaatttattttttttaaatatatttgttcacacactggaaagtggctttcagGCTGAGGACATCGCTCTGCCTGCAATTTAAGCCACATCATATTGCGGCAGGTGCCATTTTCCTTGCTGCCAAGTTCTTGAAAGTGAAGCTTCCATCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC