Sequence
atgc intronic sequence ATGC exonic sequence...acatttacatggacatatgtataaatttattattggttgaacctggcacctatcaacattaaaaacttaatatttaacttctcattttgttgatcttcagAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAGCCCACCCTTGCTCCAGTGACTGTTGAGCGAACTATGACTACCA
Basic information
species | Glycine max |
transcript | GLYMA20G35720.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g29450.1 (Oryza sativa), 3'ss of exon 7
-----------------------------------------------------------acatttacatgg--acatatgtataaatttattattggttgaacctggcacctatcaacatt--aaaaacttaatatttaacttctcattttgttgatcttcagAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAGCCCACCCTTGCTCCAGTGACTGTTGAGCGAACTATGACTACCA
| |||| || | | ||| | ||| | | || ||||| | | || | | | | | | ||| || | ||| | | | | |||||||| ||||| |||||||||||||| ||| |||| | ||||||||| || | ||||| || |||||||| || | |||||||| || ||||| || |
gtattaagactgtataagataacatataaggctactgtgttctccttttgctttgagcaaaatttcagtgctttcttttgttttaatctgctgatgtaaaaaccttttattgaccactgctccatagattgtttgcttagtttgt-attacat-gctttgcagAAAGGTGGTGGTACTATTGATCTTGAGCCTCGCCTAAGCCATACATCAGCTGTGGAGCCTACACTTGCTCCGGTTGCGGTTGAGCGCACAATGACAACAA
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G464000_T02 (Zea mays), 3'ss of exon 6
---------------------acatttacatggacatatgtataaatttattattggtt----gaacctggcacctatcaacatt--aaaaacttaatatttaacttctcattttgttgatcttcagAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAGCCCACCCTTGCTCCAGTGACTGTTGAGCGAACTATGACTACCA
|||| || | | | ||| || || | ||||| || || | || | | | | ||| ||||| ||| | || | |||||||| ||||| || |||||||||||||| |||||| || |||||| || | ||||| || ||||||||||| | |||||||| || ||||| || |
gcaagggtgtgacagtgtagagcattactgtgtctcctttttttgattcatggttaccttttgaaaccttatactgattattgttgcacaggatgtttgcttagcttct--tttacattatttgcagAAAGGCGGTGGCACCATTGATCTTGAACCACGCCTTAGTCACACATCAGCTGTGGAGCCTACACTTGCTCCAGTTGCGGTTGAGCGCACAATGACGACAA
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G08450.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------acatttacatggacatatgtataaatttattat-tggttgaacctggcaccta----tcaacattaaa-aacttaatatttaacttctcat------tttgttgat----cttcagAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAGCCCACCCTTGCTCCAGTGACTGTTGAGCGAACTATGACTACCA
| ||| || | | | || ||||| | | || | | || | |||| | || | | |||| || || | || |||| | |||||||||||||| |||||||| || ||||||| ||||||||| | |||||| | ||||| || ||||| ||| || ||||||| || ||||||| ||||
gtgatttgacatgtgccattatgtgtctttctaatttccttgattatcttctcccactatgtgcgtaatatctagttttaagtgaatttgtgtaaaactccttatggaaattctgatgatatgattccagAAAGGAGGTGGGACTATTGAACTGGAACCTTCCCTTACACACTCCTCAACTGTGGAGCCAACTCTTGCACCAATGGCTGTTGAAAGATCTATGACCACCA
upper sequence: GLYMA20G35720.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv07s0130g00270.t01 (Vitis vinifera), 3'ss of exon 6
acatttacatggacatatgtataaatttattattggttgaacctggcacctatcaacattaaaaacttaatatttaacttctcattttgttgatcttc---agAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAGCCCACCCTTGCTCCAGTGACTGTTGAGCGAACTATGACTACCA
|| || ||| |||| || | || || | | ||| || | | ||| | || || | ||| || | ||| |||||||||| || || ||||||||||||||||| || ||||||||||||||| | ||||| || |||||||||||| |||||||||| || |||||||| |
--ccttgaataatcatg-atataggttcctatctgttttctgttagtcgttattaatgcttcattctttttgcttcctttttttcttttttctttttctctagAAAGGAGGCGGGACCATTGATCTTGAACCTTGTCTAACACATACATCAACTGTGGAGCCTACTCTTGCTCCAGTGGCTGTTGAGCGTACAATGACTACAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcacctatcaacattaaaaacttaatatttaacttctcattttgttgatcttcagAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAGCCCACCCTTGCTCCAGTGACTGTTGAGCGAACTATGACTACCA
cttctcattttgtt CT-rich tract
aacattaaaaacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatttacatggacatatgtataaatttattattggttgaacctggcacctatcaacattaaaaacttaatatttaacttctcattttgttgatcttcagAAAGGAGGTGGAACTATTGATCTTGAACCTTGCCTTACACATACATCAACTATTGAGCCCACCCTTGCTCCAGTGACTGTTGAGCGAACTATGACTACCA
- - - -catggac
- - - - - - - - - - - - - - - - - - - - -cctggca
- - - - - - - - - - - - - - - - - - - - - - - - - -atcaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taaaaac