Sequence
atgc intronic sequence ATGC exonic sequencegtctgttgaatgtatactacttccttttcagggatatgataaatattaaactaacaaattttaacatgcatactatagGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
Basic information
species | Glycine max |
transcript | GLYMA18G48380.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G48380.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g58560.1 (Oryza sativa), 3'ss of exon 2
----gtctgttgaatgtatactacttccttttcagggatatgataaat---attaaactaacaaattttaaca-----tgcatactatagGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
|| |||| | | || | | ||| | || | | | | | | | || || | | | |||||||||||| || ||| | |||||||| |||||||| || ||||| || ||| | ||||||| ||||||||||||||||||
gtaggtttgtttacacgaccatatgcctggtacagcatgttaatgtgtggaaatcagttgtgagttgtttgcactgtctttttgttgcagGCTTTGATGCCATCTCTGATTCCAAGTATACTAGTGATGTGAACTGGGGCTGCATGGTCAGAAGCAGCCAGATGCTGGTTGCTCAG
upper sequence: GLYMA18G48380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G410085_T01 (Zea mays), 3'ss of exon 1
gtctgttgaatgtatactacttccttttcagggatatgataa-atatt---aaactaacaaattttaacatgcatactat---agGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
|| || |||| | | | | || || || | | | || || ||||| | | | |||||||||||| || ||| ||| || |||||||| || ||||| || ||| || |||||||||| |||||||||||||||
gttagtctttgcaggactatgtgtgtggtggaaacataattgcatgtccacaggtggctagatattgacatgttaattgtcccagGCTTTGATGCAATATCTGATTTCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG
upper sequence: GLYMA18G48380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G064212_T02 (Zea mays), 3'ss of exon 2
gtctgttgaatgtatactacttccttttcagggatatgataa-atatt---aaactaacaaattttaacatgcatactat---agGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
|| || |||| | | | | || || || | | | || || ||||| | | | |||||||||||| || ||| | ||| || |||||||| || ||||| || ||| || |||||||||| |||||||||||||||
gttagtctttgcaggactatgtgtgtggtggaaacataattgcatgtccacaggtggctagatattgacatgataattgtcccagGCTTTGATGCAATATCTGATTCCAAGCTAACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGCAGTCAAATGCTGGTTGCTCAG
upper sequence: GLYMA18G48380.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G173682_T01 (Zea mays), 3'ss of exon 1
--------------gtctgttgaatgta-tactacttccttttcagggatatgataaatattaaactaacaaattttaacatgcatactat---agGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
| ||| | ||| | | | ||||| | | | || |||| | || |||||| || | | ||| |||||||| || | | | ||| || |||||||| || ||||| || ||| || |||| |||||||||||||||||||||
gttaagctttgcaggactgc-gcttgtggtgaaaacttgttttcgtgtgcacgggtgcctagaagctaa---gtattgacatgcttattgtcccagGGTTTGATGCAATACCTGGTTCCAAGCTCACTAGTGATGTGAACTGGGGATGCATGGTTAGAAGTAGTCAGATGCTGGTTGCTCAG
upper sequence: GLYMA18G48380.1 (Glycine max), 3'ss of exon 2
lower sequence: AT3G59950.2 (Arabidopsis thaliana), 3'ss of exon 2
gtctgttgaatgtatactacttccttttcagggatatgataaatattaaacta---acaaatt--ttaacatgcatactatagGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
| ||||| || | || ||| | | | || ||||| ||| | | | | || | ||| ||||| |||||||||| |||| ||||| |||||||| || |||||||| |||||||||||| | |||||||| | || |||
-------gtttgtatgct-cccccccctcaaactca-aaccagcataaaactgttgacagaatactcactgtggcatttccagGTTTTGAGCCTATTGGAGACACAACTTATACTAGTGATGTAAACTGGGGTTGCATGCTTCGAAGCGGCCAGATGCTCTTCGCACAG
upper sequence: GLYMA18G48380.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0215g00030.t01 (Vitis vinifera), 3'ss of exon 3
-------gtctgttgaatg---tatactacttccttttcagggatatgataaatatta---aactaacaaattt-----taacatgcatactatagGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
||| |||| | || | ||| | | | ||| | |||| | || | | || | | || |||||| ||||| |||||||| ||| |||||| || |||||||| ||||||||||| ||||||||||| ||||||||||| ||||| |||
gtgcttcacatgtaaaatggtgctttctttcttcttcttattgttattagttgtattgctcacctgttgcttctctctctatccttgattttatagGTTTTGAGGCTATTGGGGATTCAAAGTTAACTAGTGATGTGAATTGGGGTTGCATGCTTCGAAGTAGTCAGATGCTTGTTGCACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttttcagggatatgataaatattaaactaacaaattttaacatgcatactatagGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
atatgataaatattaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtctgttgaatgtatactacttccttttcagggatatgataaatattaaactaacaaattttaacatgcatactatagGCTTTGATGCTATTGGAGATACAAAGTATACCAGTGATGTTAATTGGGGTTGTATGCTTCGAAGCAGTCAGATGCTGGTTGCTCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG