Sequence
atgc intronic sequence ATGC exonic sequence...ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
Basic information
species | Glycine max |
transcript | GLYMA14G06340.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 5
---ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
| | ||| | | | || | || | || || || | || || | | | | | | ||| | ||||| ||||| |||| |||||||| ||||||||||| || |||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||||||
atatgctacacctatgctggagcagttcttaaaagtttattac-gtaatgct--ttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 5
---ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
| | ||| | | | | || | || | || || || | || || | | | | | | ||| | ||||| ||||| |||| |||||||| ||||||||||| || |||||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||||||
atatgctacacctatgctggaacagtttttaaaagtttattac-gtaatgct--ttgttctatatcatcctaacattgatgtgctctctttttcacccatcagAGGCCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTGGATCAGCAACGTAGTCAGGCACTTGAAGCCCATGCAGCATCCTTTGCATCATTTAAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 4
-ttatctgtgtataattgtataag--aattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA-
| | | || | |||| | | | | || | | ||| | || || | ||| | | || || | ||| |||| ||||| |||| |||||||| ||||||||||| || || |||||||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||||
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtg--cttctcatatttgtatgccctccttttgacgcaac-cagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAGG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G057576_T01 (Zea mays), 3'ss of exon 4
-ttatctgtgtataattgtataag--aattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
| | | || | |||| | | | | || | | ||| | || || | ||| | | || || | ||| |||| ||||| |||| |||||||| ||||||||||| || || |||||||| ||||| ||||| |||||||| ||||| ||||| ||||| ||||||
cggactaaaagaaatttctgtaagtcagtaattagtaattacacaatactttgttgtatgtg--cttctcatatttgtatgccctccttttgacgcaac-cagAGACCACAACTGGTGAAGGGAAATATGCAACTTTTTTCTGTCGATCAACAGCGTAGCCAGGCGCTTGAAGCCCATGCAGCATCTTTTGCAACATTTAAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 5
ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccat-attattt-tgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
|| | | ||| | | | || | | | | || | ||| | || || ||| ||||| | | ||||||| |||||||||||| ||||| ||||| |||||||| ||||||||||| || |||||||| ||||| || ||||||||||| ||||| || |||||
gtaagtttactgcgccacatattaggtcaaaaaaagacatcaaaactgctttcatgttgtagattcttgactgatcttgtcattattatctgttttctgtagAGACAACAATTGGTAAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGTCAGGCCCTTGAGGCACATGCTGCATCGTTTGCGCAGTTTAAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 5
---ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
| || | | |||| || ||| || || | | | | | || | |||||| | | | |||||| | | ||||||| |||||||||| || ||||| ||||| |||||||| ||||||||||| || || ||||| |||||||| ||||||||||| ||||| || |||||
gtagggttcctgcaccac-gtattagg-ttg-aattaagacatcataacggcagtcatgttg-tatatttttgacggaatcttgtcattattatcctctgtagAGACCACAATTGGTGAAAGGAAATATGCAGCTTTTCTCTGTGGATCAACAGCGGAGCCAGGCCCTTGAAGCACATGCTGCATCTTTTGCTCAGTTTAAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 5
---ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatat--tattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
|| | | | | |||| ||| | | | | | || ||| | | | || || ||| |||||| || ||||| || ||||| |||| | || || || || ||||| |||||||| || || || || |||||||| |||||||||||||||||||||||||| ||| ||||||
ttgttgttt-tacttggttgttgggaaatc----tttctcctcagttttttcagagatttcctggtgttctgattttaatttccacatcctatttatgcttacagAGGCCACAGCTTGTCAAAGGGAATATGCAGCTTTTCTCTGTTGAACAGCATCGTAGTCAAGCTCTTGAAGCTCATGCTGCATCATTCGCCACGTTTAAA
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S7_102V6.1 (Physcomitrella patens), 3'ss of exon 5
ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
| ||| | | | | |||| | || | | | | | | | | | || || | | |||| | || || || || | ||| | || || ||||||||||| | || |||||||| || || | |||||||| ||||||||||||||||| |||||||| |
atctctcctcagcaacctcttgaaattttaattatcgtttagagttggttcctttctcatttaacactgcattgacagttcttatttctctggttttcagCGGCCCCAACTTGTGAAAGGAAACATGCAGTTGTTTTCAGTGGACCAGCAGAGGAGTCAGGCGCTTGAAGCTCATGCTGCGTCATTTGCTTCCCACCAG
upper sequence: GLYMA14G06340.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 5
ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
| || || | ||| | || | | | | | | | ||| | ||||| |||| || |||||||||||||| || ||||| ||||| || || ||||| ||| | ||||||||||||||||| || || ||| ||
----------------------------------------------gtatccatttcttgaaaagtttcttgtagctaacaaagaaactct----tttagCGTCCACAACTGGTGAAAGGAAACATGCAACTCTTTTCAGTCGATCAGCAGCGAAGTCAAGCTTTGGAAGCTCATGCTGCATCTTTCGCTACATTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
ttatttt CT-rich tract
tattttggtttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttatctgtgtataattgtataagaattgtgatcttttcaccgtgattttaacaaacctgatctattttggtttatttttccatattattttgcattgtagAGGGCACAATTGGTAAAGGGAAACATGCAACTTTTCTCAGTGGATCAACAACGTAGTCAGGCTCTTGAAGCTCATGCTGCATCATTTGCCCAATTTAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- atctgtg
- - - - - - - - - - - - - - - - - - - - - - - - - acaaacc