Sequence
atgc intronic sequence ATGC exonic sequence...ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaatccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
Basic information
species | Glycine max |
transcript | GLYMA07G11470.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g50120.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------ctcttcaatcctcctctaccaggattgtgtat---gatttatgaag----------ttgaatatat----ttaagtattg---cagtacgtg----tacgatttcaa----atccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
| ||| | | || | || | | | ||| ||| || |||| || | ||| |||| || || ||| ||||| | || ||| ||||||||||| ||||| |||||||| |||||||| | ||||| ||||||||||| |||| | || |||||| | ||||| || |||||||| ||||| |||||||
gtaagggaatttccatttaacatggtgatggctatattattttttcttccaacattgttatattactatgatatgtttggatcaatgtagcaacagtgttttgagaatgttctcttagacattgtcgcattaggtgatatcttgatttatattttgtcattggcttttgcagTACACCCCTGCAATTGATATTTGGAGTGTAGGATGTATATTTGCAGAGCTGCTTACAGGAAAGCCACTCTTTCCAGGGAAAAATGTTGTGCATCAATTGG
upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g45620.1 (Oryza sativa), 3'ss of exon 3
-ctcttcaatcctcctctaccaggat-tgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaatccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
| || | ||| | | | || | || || ||| ||| || || | | || | |||||| ||| |||||||||| || || |||||||| ||||||||| | || || |||||||| |||||||| | || |||||| | ||||||||||| ||||| || || |||||||
atgccatgctcttgaactatcgatacatatgcttagcataccaatttggataatttcaaatgcacttgcaccatactaaactcaaatg--tgttttttgcagTACACTCCTGCAATTGATATTTGGAGCGTCGGTTGTATATTTGCTGAAATGCTTATGGGAAAGCCACTTTTTCCTGGAAAGAATGTGGTACATCAATTGG
upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G062761_T02 (Zea mays), 3'ss of exon 4
ctcttcaatcctcctctac-caggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaatcc----ttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
| | | | | ||| || | | || |||| ||| | ||| | | || | || || | | | || |||| || ||||||||||| || || || ||||| ||||||||| | || || |||||||| ||| |||||| ||||||||| | ||||| || || ||||| ||||| || ||||
-tacttgaacagtgtgtacatagtgtggagtttgatgtatcagcttgttt---tacaaattttatagaat-cacaaggttctgaatctggcattaacttttgcagTACACTCCTGCCATTGATATTTGGAGCGTAGGGTGTATATTTGCTGAATTGCTCACAGGGAAGCCACTCTTTCCAGGGAAGAATGTTGTGCATCAGTTGG
upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G18040.2 (Arabidopsis thaliana), 3'ss of exon 3
---ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaat----ccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
| |||| ||| | | ||| | | | | ||| | | ||||| | || | | | | | | || | | |||||||||| || || ||||| || |||||||| ||||||||||||||||||||||||| ||||||||||||||||||||| || ||||| |||||||||||||
gtaaaatgcaattctctattttcttttttgcaaaagttgtctga---ttcacatattatgacaccacaacctgaggttaaaacggattattgctttctttgctgcagTATACTCCTGCCATTGATATATGGAGCATAGGATGCATATTTGCAGAAATGCTCACTGGGAAGCCATTGTTTCCTGGGAAGAATGTGGTGCACCAATTGG
upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G73670.1 (Arabidopsis thaliana), 3'ss of exon 4
---ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaatccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
|| || || || | || ||| | | | ||| || ||| ||| | | | | || | ||| | ||||||||||| || ||||| ||||||||| |||| ||||||||||| |||||||| |||||||| | |||||||| |||||||| || ||||||||||
ccacttttgtatgaaggcctgctctagttagctatctacaagtgtgcaggataaggtttg--attacagatctgatgctaactcta-cttttgcgaaatacagTATACCCCTGCGATTGATATTTGGAGCGTTGGTTGCATATTTGCTGAAATGCTATTAGGGAAGCCGCTATTTCCTGGCAAAAATGTGGTTCACCAATTGG
upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv17s0000g02570.t01 (Vitis vinifera), 3'ss of exon 4
ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttc--aaatccttgtc--ttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
|| || ||| | || ||| | | | | ||| ||| |||| | || | | ||||| ||| |||| || |||| ||||| || || || ||||| ||||||||||| ||||||||||||||||||||||| | || || || ||||||| || ||||||||||||||||| ||||
-cttttgatgaaatatgacctctttggtttataaaatttaagtggagttatgttt---tattaaactatatatcaaatttcttaaaaccttctccatttttcagTACACTCCTGCGATTGATATTTGGAGCATAGGATGCATATTTGCAGAAATGCTTACAGGAAAACCGCTGTTTCCGGGGAAAAATGTAGTGCACCAGTTGG
upper sequence: GLYMA07G11470.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ26549 (Selaginella moellendorffii), 3'ss of exon 4
ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattg--cagtacgtgtacgatttcaaatccttgtcttt-tgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
|| ||||| | | | || ||| | | | | |||||||||| || ||||| ||||| ||||||||||| ||||||||||| || | ||| | |||||||| ||||||||||||| || || || || | |
-------------------------------------------------gtaagaggatattggttcatttttttctgacgccaagtgatctcttgtatgcagTATACTCCAGCAATCGACATATGGAGCATTGGTTGCATATTTGCTGAGACAATCACTCGGAAGCCACTGTTTCCTGGAAAGAACGTTACTCATCAGCTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaatatatttaagtattgcagtacgtgtacgatttcaaatccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
tccttgtcttttgc CT-rich tract
tatttaagtatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ctcttcaatcctcctctaccaggattgtgtatgatttatgaagttgaatatatttaagtattgcagtacgtgtacgatttcaaatccttgtcttttgcagTATACCCCCGCAATTGACATTTGGAGCATTGGATGCATATTTGCAGAAATGCTCAGTGGGAAGCCATTGTTTCCTGGAAAAAATGTAGTGCACCAATTGG
ctcttca
- - - - - ctcctct
- - - - - - - - - - - - - -tgtatga
- - - - - - - - - - - - - - - - - - tatgaag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcagta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgtgtac