Sequence
atgc intronic sequence ATGC exonic sequencegtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatgaagctaatgcaagtgtatggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
Basic information
species | Glycine max |
transcript | GLYMA01G34560.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 3
----------------------------------------------------------------------gtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatga--agctaatgcaagtgtatggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
| | | ||| |||| | | | || || | | || | | || | || | || ||||||||| ||||| || || |||||| | ||||| | ||| ||||||||||| || || |||||||| |||||||| || || || |||||||| ||||||||
gtggatgttattccatagttatttctatatgtgtagttgttggtgggaatttgctggatgctgtcctttgccgtatgactcgctgctgttctgttg-catatttgattttatccatttacttatctgtattggtcgattgatttatatgaatggcagGAGGGTATCTCTCTATTTAATCGAAAGCCCAGGAAGGGAATTGAGTTCCTAATAAATGCCAACAAGGTGGGGGAATCACCTGAGGAAATTGCTGCTTTCT
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 3
----------------gtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatgaagctaatgcaagtgtatggc--agGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
|| || | || || | || ||||| ||| | | | | | | | |||| | || ||| || | |||||||||| || ||||||||| ||||||| | ||||| ||||||||||| |||||||| ||||||||||| || || || |||||||| | |||||
gtaagaacttaaagatgtttgtgtattatgcagattattgtag-aaagtgacattttataatttttctgtggtcgttaatgctattttaaatgtttgtcccagGAAGGTATTTCTCTTTTTAATCGGAAGCCAACTAAAGGTATTGAGTTTCTCATCAATGCGGGTAAGGTGGGTGAATCTCCTGAAGAAATAGCAGGTTTTC
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaaacaaatgaacaaggttttgttaataaagtat--atctttgctgtagcttttttaccaa----tga--agctaatgcaagtgtat----ggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
||||| | || |||| || | || | |||| || ||| | || ||| |||| || | ||| ||||||||||||| || |||| || ||| ||||||||||| ||||| ||| | ||||| || || |||||||| || ||||||||||||||||| |||||||
gtaaaagtttacctaaagtttgattcagcgctcattgacttttgtctcagtctttcagctaaaacctgattagctgatttgtttttattaatggcagGAAGGTATTTCTATTTTCAACCAGAAACCTAAGAAAGGTATTGAATTTTTAATCAAGGCAAACAAGGTGGGGGACTCGCCAGAGGAAATAGCAGCTTTTC
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 3
gtaaacaaatgaacaaggttttgttaataa--agta--------tatctttgctgtagcttttttaccaatgaagctaatgcaag-tgtatggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
||||| | | ||| ||||| || |||| | | || | | | || || ||| |||||| || | ||||||||||||||| | ||||| ||| |||||||||| |||||||||||||| || || ||||| || |||||||| | | |||||||| ||||| ||||| |
gtaaatgcaagg-caaccttttgggtgcaagcagtactatcttctgttctttcaattacccagttctcatggaatctaatgtaaaattcctggcagGAAGGTATAGCTCTTTTCAATCGGAAGCCTAAAAAAGGAATTGAGTTCCTTATTAATGCAAATAAGGTGGGAAACACACCAGAGGAGATAGCAGCTTTCC
upper sequence: GLYMA01G34560.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ24773 (Selaginella moellendorffii), 3'ss of exon 3
gtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatgaagctaatgcaagtgtatggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
|| | | || || ||| || | || | || || | ||||||||| || || ||||| ||| ||||||||| ||||| ||| |||| ||||| |||||||||||| | || |||||||| |||| ||||| | |||
---------------------------------gtactgaagttctatgcttcttatcat--attctcacgctagaaaactgcagGAAGGCATTTCCCTTTTCAATCGGAAGCCTAGCAAAGGCATTCAGTTCCTGATTAATGCCAAGAAGATCGGCGATTCGCCGAAGGAGATAGCAGGATTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agtatatctttgctgtagcttttttaccaatgaagctaatgcaagtgtatggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
agctaat putative branch site (score: 3)
tttttta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaacaaatgaacaaggttttgttaataaagtatatctttgctgtagcttttttaccaatgaagctaatgcaagtgtatggcagGAAGGTATATCACTTTTTAATAGGAAGCCTAAGAAAGGAATTGAGTTTCTGATCAATGCCAAGAAGGTGGGTGATTCGCCAGAGGAAATAGCTGCTTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT