Sequence
atgc intronic sequence ATGC exonic sequencegtaatgattcttttaacttgcagtcattttgttccttatttttgtttttttttttttttttggtgtttctcatttccctgttttctcgataaaagaaaaatgcttcttctaagttctaattttatatccctccttacttctgaagGAAATAGATATAGCTTGCCAAATTCAAGGATAATGATTCACCAACCGCTTGGTGGAGCTCAAGGAGGACAAACTGACATAGATATACAG
Basic information
species | Glycine max |
transcript | GLYMA19G40480.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G02560.1 (Arabidopsis thaliana), 3'ss of exon 7
gtaatgattcttttaacttgcagtcattttgttccttatttttgtttttttttttttttttggtgtttctcatttccctgttttctcgataaaagaaaaatgcttcttctaagttctaattttatatccctccttacttctgaagGAAATAGATATAGCTTGCCAAATTCAAGGATAATGATTCACCAACCGCTTGGTGGAGCTCAAGGAGGACAAACTGACATAGATATACAG
|| | | || | ||| | | | | |||| || | ||| || | | | | | | | | | || ||| |||||| ||||| || | ||||| |||||||||||||| || || |||||||||||||||||||| || ||||| ||||| || || |||
-------------------------------------------gtagtctcttaatcctttca-atcattagtaaaaatcttttagtgaagtcttatgaatttcatttttctgatgtgagtcatgctttattcgtaaaactgtagGAAAAAGATACAGTCTACCAAACTCAAGGATAATGATCCATCAGCCGCTTGGTGGAGCTCAAGGTGGCCAAACCGACATTGACATTCAG
upper sequence: GLYMA19G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv07s0005g01530.t01 (Vitis vinifera), 3'ss of exon 7
gtaatgattcttttaacttgcagtcattttgttccttatttttgtttttttttttttttttggtgtttctcatttccctgttttctcgataaaagaaaaatgcttcttctaagttctaattttatatccctccttacttctgaagGAAATAGATATAGCTTGCCAAATTCAAGGATAATGATTCACCAACCGCTTGGTGGAGCTCAAGGAGGACAAACTGACATAGATATACAG
|| | |||| | |||| || || ||| || | |||| ||| | | | | || | | || | | | | | || ||| |||||||||| ||||||||||||||||| |||||||| ||||| || || || || |||||||||||||| || ||||||||||||||||| |||
------------------------------gtaagtaatttcc---taggcttttgttgttagtggtttggagttccac---ttcgtggcatatgctttttggtg-tgctttgacatgtgtctgtcacctccctcttaactgaagGAAAAAGATATAGCTTGCCAAACTCAAGGATCATGATCCATCAGCCTCTCGGTGGAGCTCAAGGTGGGCAAACTGACATAGATATTCAG
upper sequence: GLYMA19G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ24258 (Selaginella moellendorffii), 3'ss of exon 6
gtaatgattcttttaacttgcagtcattttgttccttatttttgtttttttttttttttttggtgtttctcatttccctgttttctcgataaaagaaaaatgcttcttctaagttctaattttatatccctccttacttctgaagGAAATAGATATAGCTTGCCAAATTCAAGGATAATGATTCACCAACCGCTTGGTGGAGCTCAAGGAGGACAAACTGACATAGATATACAG
|| |||| | | | ||| || || | |||| | | | || || || |||||| | ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||| || | ||||| || || |||
-------------------------------------------------------------------------------gtattctacacactt---acatgattttttt---ttctcac---gtctgccattttgaaactccagGAAAGCGTTATAGTTTACCAAATTCTAGGATCATGATTCACCAGCCGCTCGGTGGCGCTCAAGGACAGCAGTCCGACATTGAGATCCAG
upper sequence: GLYMA19G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ35520 (Selaginella moellendorffii), 3'ss of exon 6
gtaatgattcttttaacttgcagtcattttgttccttatttttgtttttttttttttttttggtgtttctcatttccctgttttctcgataaaagaaaaatgcttcttctaagttctaattttatatccctccttacttctgaagGAAATAGATATAGCTTGCCAAATTCAAGGATAATGATTCACCAACCGCTTGGTGGAGCTCAAGGAGGACAAACTGACATAGATATACAG
|| ||| | | | | | || |||| | ||| || | |||| |||||| | ||||| || |||||||| ||||| ||||||||||| ||||| ||||| ||||||||| || | ||||| || || |||
-------------------------------------------------------------------------------gtactctacacacttaatgatttttttttctcacgtctgccattttgaaactcc----------agGAAAGCGTTATAGTTTACCAAATTCTAGGATCATGATTCACCAGCCGCTCGGTGGCGCTCAAGGACAGCAGTCCGACATTGAGATCCAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaagaaaaatgcttcttctaagttctaattttatatccctccttacttctgaagGAAATAGATATAGCTTGCCAAATTCAAGGATAATGATTCACCAACCGCTTGGTGGAGCTCAAGGAGGACAAACTGACATAGATATACAG
tccttac putative branch site (score: 2)
ttttatatccctcctt CT-rich tract
ttctaagttctaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatgattcttttaacttgcagtcattttgttccttatttttgtttttttttttttttttggtgtttctcatttccctgttttctcgataaaagaaaaatgcttcttctaagttctaattttatatccctccttacttctgaagGAAATAGATATAGCTTGCCAAATTCAAGGATAATGATTCACCAACCGCTTGGTGGAGCTCAAGGAGGACAAACTGACATAGATATACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA