Sequence
atgc intronic sequence ATGC exonic sequencegtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagattagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaacgtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
Basic information
species | Glycine max |
transcript | GLYMA13G43680.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagattagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaacgtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
| | | | | | | | ||| || ||| || ||| || | || | | |||| |||||||||||| ||| |||| ||||||||||| ||||| |||| ||| ||||| |||||||||||||||||
--------------------------------------------------------------------------gtaatgcagtctcctttgatgctcgatttcatccttaatcattcttattcggg--actgtat-tgacacgcttctttg--ttttgatcagCGTAAGTTTGCTCAAAGATCAGAAAGAGTCAAATCTGTAGATCTCCATCCAACAGAGCCATG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 2
lower sequence: AT3G15980.3 (Arabidopsis thaliana), 3'ss of exon 2
gtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagattagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaacgtgttattttgat-ttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
||| | | | || | || ||| | | | || || | ||| | ||| || | || | || |||||||||| | ||| |||| ||| ||||||||||||| |||| ||| ||||||||||| || || |||||
-----------------------------------------------------------------------------gtattgcttatctttcaactttctgcttctgttattttatta--ttatagctg-tggtcataatttgcttttgttatgttttgatcagAGAAAGTTTGCTCAACGATCAGAGAGAGTCAAATCTGTTGATCTGCATCCTACTGAACCATG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv09s0002g04810.t01 (Vitis vinifera), 3'ss of exon 2
gtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagat-tagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaacgtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
|| |||||| || || ||||| | | || || |||| | ||||||| | | | |||| |||| || ||| | || | ||| ||| ||||| |||||| | || || |||||||||||||||||||| |||| |||||||||||||||| | ||||||||
-----------------------------gtacgcttgttt---attccctttgaattgatttctatgt-acagattagatctcgatttgtttaatgtttaa--tagt-tgaa-gtattgatgtcattttgcttctggtaa------------attttggatcagAGGAAACTCGCGCAAAGATCAGAGAGAGTAAAATCTGTGGATCTGCATCCATCTGAGCCATG
upper sequence: GLYMA13G43680.2 (Glycine max), 3'ss of exon 2
lower sequence: PP1S79_180V6.1 (Physcomitrella patens), 3'ss of exon 2
gtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagattagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaac-gtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
||| || | || || ||| | | | | | |||| || || ||| | | || || | ||| | ||| || || |||||| || || |||||||| || ||| |||| || ||||||||||| |||||||||||||||||
-------------------------------------------------------------aattgaattcttctcatcatcagcagtgttgcagagtgtg--aagtggtgattttatgcctgcacaggttttgtgctgatagtgctgattttcttatt--tcagCGGAAACTCGCGCAAAGGTCTGAGCGAGTTAAGTGTGTGGATCTTCATCCAACAGAGCCATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatgttttgctttctggctacttaatctaacgtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
ttttt CT-rich tract
ttattttgatttttga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaattgttttttgttctgattcaatgtttatttgtttttggttgccgacaaattgttgatttcgttacctgcgagattagatttgtcggaaactaagcctagtgtgaatgttttgctttctggctacttaatctaacgtgttattttgatttttgatcagCGCAAGCTTGCGCAAAGATCAGAGAGAGTGAAATGTGTGGATCTGCATCCAACAGAGCCATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA