Sequence
atgc intronic sequence ATGC exonic sequence...ttgtttcgatattattcctgatgccatatgctgtaaccttatcaatgtaagaccagtggatgtttctgtttcttacataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG
Basic information
species | Glycine max |
transcript | GLYMA20G38750.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38750.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G021687_T01 (Zea mays), 3'ss of exon 3
------ttgtttcgatattattcctgatgccatatgctgtaaccttatcaatgtaagaccagtggatgtttctgtttcttacataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG
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aacagctttgttcattggaatgtctaaaagcctgcagtataatgccatgtatatatacagaaatagtgtctatgaataattcg------atttcatctgtgttcagGCGACATGTGTGGTGGCACAGGGAAATGGAAGGCCCTCAATCGGAAGAGGGCGAAAGATGTTTATGAATTCACCGAGTGCCCGAATTGCTACG
upper sequence: GLYMA20G38750.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G34860.2 (Arabidopsis thaliana), 3'ss of exon 3
ttgtttcgatattattc-ctgatgccatatgctgtaaccttat---caatgtaagaccagtggatgtttctgtttcttacataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG
|||| || |||| ||| | |||| || | | | | | | || | | | | ||| | | | ||| || | || ||| ||||||||||||||| |||||||||||||||||||| ||| | || || || |||||||| || || ||||| || |||||||| ||||| |
---gttcgtaatgattctctgtttccatttgatatgatgcaaaatgcctcatgagcttactactgatacccatttggttta-attggattttgttatgatatagGTGATATGTGTGGTGGTACAGGAAAATGGAAAGCTCTCAACCGAAAACGTGCGAAAGATGTATATGAGTTTACGGAATGTCCAAACTGTTACG
upper sequence: GLYMA20G38750.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0004g01100.t01 (Vitis vinifera), 3'ss of exon 3
-------ttgtttcgatatt----attcctgatgccatatgctgtaaccttatcaatgtaagaccagtggatgtttctgtttcttacataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG
|||| | || || | | | | | || ||| | | || | || || | | || | |||||| || ||| |||||||||||| ||||||||||||||| || ||||||||||||||||| ||||| || || ||||||||||||||||| |||||||| || |||||||||||||
tacctacttgtcatggacttcggtgtttcctaaacaaccta-tgcaacacttttaa-gcaacac-atggaataatgctgtttattg--------atttgcttttcatttagGTGATATGTGTGGTGGTACGGGAAAATGGAAAGCTCTCAACAGAAAACGGGCTAAAGATGTTTACGAGTTTACTGAATGCCCAAATTGTTATG
upper sequence: GLYMA20G38750.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ07587 (Selaginella moellendorffii), 3'ss of exon 1
ttgtttcgatattattcctgatgccatatgctgtaaccttatcaatgtaagaccagtgg-atgtttctgtttcttac-ataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG
| || | || | | ||| |||| || | ||| | || | || | | | || |||||||||||| || || ||||| ||||||||||| | |||||||||||| || || || ||||| || || |||||||| ||||| || |
-------------------gtaagttgatagtcctgccctgctagtgttgttccagccacgcattcttctttgtgactggattggattcgcggtgc-cacagGTGATATGTGTGGAGGGACTGGAAAGTGGAAAGCTCTCAGCAGGAAGCGAGCCAAGGACGTGTACGAGTTCACCGAGTGTCCCAATTGCTACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtaagaccagtggatgtttctgtttcttacataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG
ttcttac putative branch site (score: 2)
tttacttttcattt putative PPT
tttacttttcattta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgtttcgatattattcctgatgccatatgctgtaaccttatcaatgtaagaccagtggatgtttctgtttcttacataccatgtttacttttcatttagATGATATGTGTGGTGGCACAGGAAAATGGAAAGCTCTTAACAGGAAGCGAGCTAAAGATGTTTACGAATTTACTGAGTGTCCAAATTGTTATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG