Sequence
atgc intronic sequence ATGC exonic sequence...atgtttatctatattatcatattaaaattgataataaatgtcaatgaatacacttagcttcatttatcatgatgttgatgctgttttaattgtgttgcagACCTCAGGTAACTATTGCAACTGCAATAATATTTTGTCATCGATTCTTTCTCCGGCAGTCCCATGCAAAGAATGACAGGAGG
Basic information
species | Glycine max |
transcript | GLYMA15G41040.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 1
atgtttatctatattatcatattaaaattgataataaatgt-caatgaatacacttagcttcatttatcatgatgttgatgctgttttaattgtgttgcagACCTCAGGTAACTATTGCAACTGCAATAATATTTTGTCATCGATTCTTTCTCCGGCAGTCCCATGCAAAGAATGACAGGAGG
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atttcctactgttttattatttttttatgcctcaaacatgagcaaatagtttataattgtttttccagcatcactgtgattatgaac-attttaattgcagGCCCCAGGTAACAATTGCTACAGCAATCATATTTTGTCACCGTTTCTTCCTTCGTCAATCCCATGCAAAGAATGACAGAAGG
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ37217 (Selaginella moellendorffii), 3'ss of exon 1
--------atgtttatctatattatcatattaaaattgataataaatgtcaatgaatacacttagcttcatttatcatgatgttgatgctgttttaat---------tgtgttgcagACCTCAGGTAACTATTGCAACTGCAATAATATTTTGTCATCGATTCTTTCTCCGGCAGTCCCATGCAAAGAATGACAGGAGG
| | ||| | || | || | | | | | || | | | || | || | || ||||| | |||| | | |||||| || ||||| |||||||| || ||||| | |||||||||||| |||| ||| ||||| |||||||||| || || ||
gtaagcttgttctcttctccttcgtcttgttcttctcggaattttctttcttttc-ttctctcactcacactcattgacggtttgatttttttttcttgttctttcgttctttgcagCCCACAGGTGACTATTGCCACCGCAATTACATTTTGTCATCGTTTCTATCTTCGGCAATCCCATGCAAGAAACGATAGATTT
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ27727 (Selaginella moellendorffii), 3'ss of exon 1
-------------atgtttatctatattatcatattaaaattgataataaatgtcaatgaatacacttagcttcatttatcat--gatgttgatgctgttttaattgtg--ttgcagACCTCAGGTAACTATTGCAACTGCAATAATATTTTGTCATCGATTCTTTCTCCGGCAGTCCCATGCAAAGAATGACAGGAGG
| | | | || | | | ||| | | | || | |||| || ||||| | | ||| || | || || | || |||||| || ||||| |||||||| || ||||| | |||||||||||| |||| ||| ||||| |||||||||| || || ||
gtaagcttgttctcttctccttcgtcttgttcttctcggatttttctttcttttc--ttctctcactcagactcattgacggtttgattttttttcttgttctttcgttctttgcagCCCACAGGTGACTATTGCCACCGCAATTACATTTTGTCATCGTTTCTATCTTCGGCAATCCCATGCAAGAAACGATAGATTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatacacttagcttcatttatcatgatgttgatgctgttttaattgtgttgcagACCTCAGGTAACTATTGCAACTGCAATAATATTTTGTCATCGATTCTTTCTCCGGCAGTCCCATGCAAAGAATGACAGGAGG
ttttaat putative branch site (score: 3)
tgttttaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtttatctatattatcatattaaaattgataataaatgtcaatgaatacacttagcttcatttatcatgatgttgatgctgttttaattgtgttgcagACCTCAGGTAACTATTGCAACTGCAATAATATTTTGTCATCGATTCTTTCTCCGGCAGTCCCATGCAAAGAATGACAGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - -caatgaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gatgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgctgtt