Sequence
atgc intronic sequence ATGC exonic sequencegtccgcatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcgttttctgactctccgatacgctcttcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCACGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
Basic information
species | Glycine max |
transcript | GLYMA01G38580.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os12g01390.1 (Oryza sativa), 3'ss of exon 1
gtccgcatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattct--ctcgtcgttttctgactctccgatacgctcttcgtttt-tgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCACGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
| || | ||| | | ||||||| | || | | | || | | | ||||||| | ||| ||| | ||||| | | || | || ||| || || ||| |||| ||||| |||||||||||||| ||||| || ||||| |||||| | || ||| | ||||||||||
------gtatcctcttctcctcttactcctccccgcgagatctcact-cgtaaccaaggcggagctaatggcgcctgactcgtatctcttctcctcgctcgatgcagCTCACCAGCCTGGGGATCGCGCCCCAGTTCGTCACCTTCACCCACGTCACCATGGAGTCGGAGAAATACATCTGCGTCCGCGAGACCTCCCCGCAGAACA
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os11g01380.1 (Oryza sativa), 3'ss of exon 1
--gtccgcatttcgccactctctcgtc-gttttccccgcaatgccttgccgcattgcccattct--ctcgtcgttttctgactctccgatacgctcttcgtttt-tgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCACGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
|| | | || | ||| | | ||||| | || || | | || | | | ||||||| | | ||| ||| | ||||| | | || | || ||| || || ||| |||| ||||| |||||||||||||| ||||| || ||||| |||||| | || ||| | ||||||||||
gtatcttcttctcttcttactcctacccactcctcccgcgagatctcccc-cgtaaccaaggcggagctaatggcgcctgactcgtctctcttctcctcgctcgatgcagCTCACCAGCCTGGGGATCGCGCCCCAGTTCGTCACCTTCACCCACGTCACCATGGAGTCGGAGAAATACATCTGCGTCCGCGAGACCTCCCCGCAGAACA
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 1
gtccgcatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcgttttctgactctccgatacgctcttcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCACGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
| || | ||| | | || | | | | | |||||| | | |||| | || | | | | | |||| | | || | || ||| ||||| || |||| || || || ||||||||||| ||||| |||||||| |||||| | || ||| ||||||||||||
-----------gtaacaccttcgccacctcgtcctc----ctcttcttctccatccattcaccca-------ctgatcgttcgttgcttgcctgtcctccgcagCTCACCAGCCTGGGCATCGCGCCGCAGTTTGTCACGTTTACCCATGTCACCATGGAGTCGGAGAAGTACATCTGCGTCCGCGAGACCTCGCCGCAGAACA
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv06s0004g06860.t01 (Vitis vinifera), 3'ss of exon 1
-----------------------------------------------gtccgcatt---tcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcg----tttt----ctgact-ctccgatacgctcttcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCACGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
|| || | | || | || | | || | ||| | || || | | || | |||| ||| | || | | | || | ||||||||| | ||| ||||||| | ||||||||||| || || ||||| || |||||||| ||||| ||||| ||||| || ||||| || |||||||||||||
gtaagttctggagctcgatttgttcgttattgtttaaattcacttcagttcgtagtagatcttggattgttctggatctgtgttacagatcattgttgagttagttgttttttagtggataattttggtgttgattgttctgtttggttcggtggaattgcagTTGTCTAGTATCGGAATTAGTCCGCAATTCATGACATTTACGCATGTGACCATGGAGTCGGATAAGTATATTTGTGTTAGGGAGACGGCGCCGCAGAACA
upper sequence: GLYMA01G38580.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ24508 (Selaginella moellendorffii), 3'ss of exon 1
gtccgcatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcgttttctgactctccgatacgctcttcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCACGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
|| | | | | ||| || | || | || | | || | || |||| | | || | || ||||| || |||| ||||||||||| || ||||| |||||||| || |||||||| ||||| || || ||| ||||||||||||
------------------------------gtgcgtattttggttttggatttatttgctagaaatcagcattggattgtctaa-----ttttgttcttggcagCTCACGAGCTTGGGCATCAATCCCCAATGCATCACTTTCAACCATGTCACGATGGAATCCGAGAAGTACATATGCGTGAGAGAGACCACGCCGCAGAACA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attgcccattctctcgtcgttttctgactctccgatacgctcttcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCACGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
ttctgac putative branch site (score: 2)
cgctcttcgttttt putative PPT
ttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtccgcatttcgccactctctcgtcgttttccccgcaatgccttgccgcattgcccattctctcgtcgttttctgactctccgatacgctcttcgtttttgcagTTGGCAAGTGTCGGAATCAACCCGCAATTCATCACTTTCACGCACGTCACCATGGAATCGGACAAGTACATTTGCGTCAGGGAAACCGCGCCGCAGAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA