Sequence
atgc intronic sequence ATGC exonic sequence...atatgctttggatcatgaaataattcctctttaaccttccatttgattttatttgaacatacttgtgtttctaatcattattatcatttaaaaataatagGGGCCCCGGTGCTACCGTGCTTATCTTGTCATGGGTTATCACCCTCTACACCCTATGGCAAATGGTTGAGATGCACGAAATGGTGCCAGGGAAAAGATTT
Basic information
species | Glycine max |
transcript | GLYMA18G01300.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G01300.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S79_71V6.1 (Physcomitrella patens), 3'ss of exon 3
----------atatgctttggatcatgaaataattcctctttaaccttccatttgattttatttgaacatacttgtgtttctaatcattattatcatttaaaaataatagGGGCCCCGGTGCTACCGTGCTTATCTTGTCATGGGTTATCACCCTCTACACCCTATGGCAAATGGTTGAGATGCACGAAATGGTGCCAGGGAAAAGATTT
|| | | || | ||||| || |||| | | || || | | || | | || | | | | | |||||| || ||| |||| ||| | |||||||| |||||||||| ||| || ||||||||||| |||||||||||| ||||| || || ||||
gtatcaaccactacaccacag-ccagttcacgtttccttccta-ttttccttccgccattgttcccttctccacaaactt-tgaggatgacgtgggtatcatgtttgtagGGGTCCAGGTCTCCTAATGCTCATCCTTTCATGGGTCATCACCCTCTTCACACTCTGGCAAATGGTGGAGATGCACGAAGCTGTGCCCGGAAAGCGATTC
upper sequence: GLYMA18G01300.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ10950 (Selaginella moellendorffii), 3'ss of exon 2
----atatgctttggatcatgaaataattcctctttaaccttccatttgattttatttgaacatacttgtgtttctaatcattattatcatttaaaaataatagGGGCCCCGGTGCTACCGTGCTTATCTTGTCATGGGTTATCACCCTCTACACCCTATGGCAAATGGTTGAGATGCACGAAATGGTGCCAGGGAAAAGATTT
| | || | | ||| | | || | | || | || ||| | | || | | || ||| | ||||| || || | || ||| | |||| ||||| ||||| |||||||| || ||||||||||| || |||||||||||||| || ||||| ||||||
accctagtcgtgtgtcgcccgcaatcctccagctccatgttcttgacaaatggttttccaacttttccaagc----aactttaaagatttttttttcgttccagGGGACCGGGGGTCCTTGTTCTTGTACTGTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT
upper sequence: GLYMA18G01300.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ25874 (Selaginella moellendorffii), 3'ss of exon 2
atatgctttggatcatgaaataattcctctttaaccttccatttgattttatttgaacatacttgtgtttctaatcattattatcatttaaaaataatagGGGCCCCGGTGCTACCGTGCTTATCTTGTCATGGGTTATCACCCTCTACACCCTATGGCAAATGGTTGAGATGCACGAAATGGTGCCAGGGAAAAGATTT
| | | | || || | || | |||| | | |||| | || | | || || | ||||| || || | || ||| | | || ||||| ||||| |||||||| || ||||||||||| || |||||||||||||| || ||||| ||||||
gtgtcacccgcaatcctcaagaactttcacagccccatgttcttgacaaatcgttttccaacttttccaagcaactttaaagatttgtttttcgttccagGGGACCAGGGGTCCTGGTTCTTGTACTCTCGTGGGTGATCACACTCTACACGCTGTGGCAAATGGTGGAAATGCACGAAATGGTCCCGGGGAAGAGATTT
upper sequence: GLYMA18G01300.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ10949 (Selaginella moellendorffii), 3'ss of exon 1
atatgctttggatcatgaaataattcctctttaaccttccatttgattttatttgaacatacttgtgtttctaatcattattatcatttaaaaataatagGGGCCCCGGTGCTACCGTGCTTATCTTGTCATGGGTTATCACCCTCTACACCCTATGGCAAATGGTTGAGATGCACGAAATGGTGCCAGGGAAAAGATTT
| || ||| | | || | | | ||| | || | ||||| || || |||||| || | || ||| |||| |||||||| |||||||||||||| ||||||||||| |||||| || || | ||
---------------------------------------------gtaacgttcgaatgttataacgtctacattttttagggtt-cttcgtttttccagGGGGCCTGGGATCTTCGTGCTCCTCCTCTCCTGGACCGTCACGCTCTACACGCTATGGCAAATGGTGGAGATGCACGAGATGGTGGAGGGCAAGCGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attttatttgaacatacttgtgtttctaatcattattatcatttaaaaataatagGGGCCCCGGTGCTACCGTGCTTATCTTGTCATGGGTTATCACCCTCTACACCCTATGGCAAATGGTTGAGATGCACGAAATGGTGCCAGGGAAAAGATTT
ttctaat putative branch site (score: 2)
ttgtgtttctaatcat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atatgctttggatcatgaaataattcctctttaaccttccatttgattttatttgaacatacttgtgtttctaatcattattatcatttaaaaataatagGGGCCCCGGTGCTACCGTGCTTATCTTGTCATGGGTTATCACCCTCTACACCCTATGGCAAATGGTTGAGATGCACGAAATGGTGCCAGGGAAAAGATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - gctttgg
- - - - - - -catgaaa
- - - - - - - - - - - - - - - - - ccttcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - acttgtg