Sequence
atgc intronic sequence ATGC exonic sequencegtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
Basic information
species | Glycine max |
transcript | GLYMA18G02040.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G128771_T01 (Zea mays), 3'ss of exon 2
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattct-ttgtatgttaaa-attgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
| ||| | ||| || | || | ||| ||| |||| | ||| | | | |||||| || | ||||||||||||||| || || || ||||| ||||| |||||||||||||| || || ||||||||||| || ||||| || |||||| |||
------------------------------------------------nnnnnnnnnnnnnnnnnnncacattac-tatttgagttttggtagctttgttagttcattttcttggagaacagttagcatttcattgttcttgctgtcagGGATACTGCAGGACAGGAGAGGTTTAGGAGTCTTATTCCAAGCTACATCAGGGACTCTTCTGTTGCGGTGGTTGTTTATGATGTATCCA
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G39890.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattc-tttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
| | | || ||| ||| | | || || ||| ||| || ||| | || | || |||| | || | ||||||||||| || ||||||||||| || ||||| || ||||| ||||| ||||||||||||||||| ||||||||||||||||| |||
------------------------------------------------------gtgagaacaatgttac-ttttgctct-ttacctaaaaact------aacatgttaatttcaaaagcaataacaaaacaagttttga-ttgaaagGGATACTGCTGGACAAGAAAGATTCAGGAGTCTAATCCCAAGTTACATCAGAGATTCTTCTGTTGCCATTGTTGTATACGATGTATCCA
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G10260.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
| | |||| | || | ||| || ||||||| || | || | | || || ||||| | ||| ||||||| ||| ||||||||||||||| || || |||||| ||||||| || ||||| || || ||||||||||||||||| || |||| || ||||| || |
-------------------------------------------tgaatggaacatcaaaatgtccatggaaattctcagcattgtgtatcaaccatgttcattcttttagttatatgtcatt-ttgaatcatatt---actgtgcagGGATACTGCAGGACAGGAGAGATTTCGAAGTCTAATACCAAGTTATATCAGAGATTCTTCTGTTGCTGTAATTGTCTATGATGTTGCAA
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G22290.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgta-tgttaaaattgtt--tcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA-----------
| ||| | || || | |||| ||| | || | | || | | || || | | | | ||| || |||||||| || || ||||||||||| || ||| | || ||||| |||||||||||||||||||||||||||||||| || ||||||||||
-----------------------------------------------------------------gtaagaaatgctgtt-ttttctagg-gcttctcgcaatgtaatattcgcaatgaggaagctaataatgtgaattttcgtttttagGGATACAGCTGGACAAGAAAGATTCAGGAGTTTAATACCAAGTTACATAAGAGATTCTTCTGTTGCAGTTGTTGTTTATGATGTAGCCAATAGACTCTCA
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0665g00040.t01 (Vitis vinifera), 3'ss of exon 2
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttg-tgtaggcacttttt-ttaacccattctttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
||| ||| || || || | | | || || ||| | | | | | ||| || | | | | || | ||||||| || ||| || |||||||||||||||| || |||||||||||||| ||||| || ||||||||||||||||||||||| ||||| || |||| || ||||| | |
-------------------------------------------gattggtttctc---aaattgtttaggtttacatgctgtagatacttgtattatttgtttatatacttctagttt-ctaaaatt--ttggcttttgaaattcacagGGATACTGCTGGCCAAGAAAGATTTAGGAGTCTTATACCAAGCTACATAAGAGATTCTTCAGTTGCTGTGATTGTTTATGATGTTGGAA
upper sequence: GLYMA18G02040.1 (Glycine max), 3'ss of exon 2
lower sequence: PP1S353_41V6.1 (Physcomitrella patens), 3'ss of exon 3
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgtatgttaaaattgtttcatatttt-aact-tcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
| | || | ||| || | | || || | || | | | | | | | ||| || | ||| ||| | | |||| | ||||||||||||||||||||||| ||| ||||||| ||||| ||||| || | ||||| || || ||||| || || || || || | |
--------------------------------------acaatttttctgtttgggggcagcagagatgaactttac-ctactggtttgtctcctctggcagacca----------attgacgttgcttcccctgctgaactgttgtagGGATACTGCAGGGCAAGAAAGGTTTCGAAGTCTAATTCCTAGCTATATCCGTGATTCATCAGTCGCAGTGGTCGTTTATGACGTGTCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctttttttaacccattctttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
ttttaac putative branch site (score: 2)
attctttgtatgttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggccatattcctctttaactcatgccacaagacctatttatatttttttttctaaaagttatattagatttcacattgttgtgtaggcactttttttaacccattctttgtatgttaaaattgtttcatattttaacttcacagGGATACTGCAGGGCAAGAAAGATTTAGAAGTCTGATTCCAAGCTACATAAGAGATTCTTCTGTTGCAGTTGTTGTATACGATGTAGCCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA