Sequence
atgc intronic sequence ATGC exonic sequence...ttcaacttaatacaaaaccttgatgcccagtctaattttatccatgtttaatgagtcactagcagcacactaagcagagaaatttcttgctaaattgcagGCTTAACGGATTAGTAGACCATTTCAAGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
Basic information
species | Glycine max |
transcript | GLYMA13G43770.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g54624.1 (Oryza sativa), 3'ss of exon 2
---------------ttcaacttaatacaaaaccttgatgcccagtctaat-tttatccatgtttaatgagtcactagcagcacactaagcagagaaatttcttgctaaattgcagGCTTAACGGATTAGTAGACCATTTCAAGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
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ctgaagcatctgtgtatgagcattgcaaggaacactattgtttagattgttatttacacatgttcacaatgttgctatt-------taa--agacaaatgcctt-------ttcagGATTAATGCTCTTTTTGACCACTTCAAGATGGCCTTGGATTGTTTCTTTGCTGTGTGGTTTGTCGTAGGAAATGTGTGGATATTTGGCGGGCGTTCTTCT
upper sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G089466_T01 (Zea mays), 3'ss of exon 2
------------------------------------ttcaacttaatacaaaaccttgatgcccagt-ctaattttatccatgtttaatgagtcac--tagcagcacactaagcagagaaatttcttgctaaattgcagGCTTAACGGATTAGTAGACCATTTCAAGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
| || | | || | || | || |||| | || | | || || | || || ||| | | ||||| |||||| | || | | | ||||| |||||||||||| ||||||| |||||||| || |||||||| || ||||| || ||||| ||||| || | |||||
gtactcatgccttctttttttccttaaaaaaatggatcggtatttacaatgaatatgtttgactgtcacttgttttgtttatttatggtgctgcaaaatggctatgcattaaagatgaatgccctgtgctat-ctgcagGATCAATGCGCTGTTTGACCACTTCAAGATGGCCCTGGATTGTTTCTTTGCCGTCTGGTTTGTTGTTGGAAACGTGTGGATATTTGGTGGCCGTTCTTCT
upper sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G80400.1 (Arabidopsis thaliana), 3'ss of exon 2
ttcaacttaatacaaaaccttgatgcccagtctaattttatccatgtttaatgagtcactagcagcacactaagcagagaaatttcttgctaaattgcagGCTTAACGGATTAGTAGACCATTTCAAGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
||||||||| | | | | | | | | | || | | | || || | | | ||||||| ||||| |||| ||||| ||||||||||| | ||||| |||||||| || |||||||| || || ||||| ||||| |||||||||||| | |||
-------------------------gtaagtctaattac-tttgtttggcctcaattaatttgggttggttagtta---acaattgttaatgactggcagGCTCAACGGGCTAGTGGACCACTTCAAGATGGCGATTGATTGTTTCTTTGCGGTGTGGTTTGTTGTGGGGAATGTATGGATATTTGGAGGTCACTCATCT
upper sequence: GLYMA13G43770.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g05120.t01 (Vitis vinifera), 3'ss of exon 2
ttcaacttaatacaaaaccttgatgcccagtctaattttatccatgtttaatgagtcactagcagca-cactaagcagagaaatttcttgctaaattgcagGCTTAACGGATTAGTAGACCATTTCAAGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
|| | || | | | | | |||| | || ||| | | | | | | | | | | | || || | |||| | | ||| | || |||||||| |||||||||||||| |||||||||||||| |||||||| || || ||||| ||||| |||||||||||| |||||
-tctgatagttaattattttaaacttttaacccttttttgtatccattcaataatttatatattgtatcggttaatgatgtagctgatttctgatacccagGTTCAGTGGAATGGTGGACCATTTTAAGATGGCCTTGGACTGCTTCTTTGCAGTGTGGTTTGTTGTGGGCAATGTGTGGATATTTGGAGGTCACTCTTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtttaatgagtcactagcagcacactaagcagagaaatttcttgctaaattgcagGCTTAACGGATTAGTAGACCATTTCAAGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
tgctaaa putative branch site (score: 2)
tttcttgct CT-rich tract
aaatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcaacttaatacaaaaccttgatgcccagtctaattttatccatgtttaatgagtcactagcagcacactaagcagagaaatttcttgctaaattgcagGCTTAACGGATTAGTAGACCATTTCAAGATGGCCTTGGATTGCTTCTTTGCAGTTTGGTTTGTAGTAGGAAATGTTTGGATCTTTGGAGGTCACACTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - caaaacc
- - - - - - - - - - -gatgccc
- - - - - - - - - - - - - - - - - - - - -ccatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - cactagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacacta