Sequence
atgc intronic sequence ATGC exonic sequence...ccttaaatcaggtaaattcatattccataaatgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
Basic information
species | Glycine max |
transcript | GLYMA13G39410.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g04814.1 (Oryza sativa), 3'ss of exon 2
ccttaaatcaggtaaattcatattccataaatgttatgaatgtaggt-ccataagtg-gacatgttcttgcaagcatttttaacttttgaattcttcat-cagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
| | | | ||| || || || || | || | ||| | || || | | | | || | | | | | ||| || |||| | ||||||||||||||||||||||| |||||||| || |||||||| || ||| ||||||||||| ||||||||||||||| || ||||| || ||
--tgatgttgccaatgatcaatatcaatgtataccatattcatttgtattgttcgtgcaatatattttattatgtttcatttaatgt-gtttgctttatgcagTATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAGAGTGAAAAACTTGTTGCAAACCTTTTCCAAATGGCTCGAGAAAACGCTCCTTCCATTATC
upper sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g04840.1 (Oryza sativa), 3'ss of exon 2
ccttaaatcaggtaaattcatattccataaatgttatgaatgtag-gtccataagtggacatgt-tcttgcaagcatttttaact-tttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
|| | | || | | | | || | || || | | | | | | | || || | | ||||| ||| || | ||| | ||||||||||||||||||||||| |||||||| |||||||| || || ||| | || |||||| | ||||| || |||| ||| || || || ||
--ttctctttcttttctttgc-tgctactgctagtactagtgcagtatgctttgttctttgtttctgtttcatgttatgttaacgattttggttttcttgcagCATATCTTCATCAGACCTTGTTTCAAAATGGATGGGAGAAAGTGAGAAACTAGTTGCTAATCTTTTCCAGATGGCCCGTGAAAATGCTCCCTCCATTATC
upper sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G088834_T01 (Zea mays), 3'ss of exon 2
---ccttaaatcaggtaaattcatatt--ccata--aatgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
| | || ||| ||| || || | ||| ||| | | | | | || | | | | || | |||| ||| ||| | | | |||| | ||||| ||||| || |||||||||||||||||||||||||| || | ||| |||| || ||| |||||||||| |||| ||||||||| || ||
tttcacttgatt-ggtcaatggatgttagcaatactaatatcctaccatttgttttctatgc---cgtatctttatga-tatttcacactgttg--ctttactgcagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGTGAGAAATTAGTTGCAAATCTGTTCCAAATGGCTCGGGAAAATGCCCCTTCCATTATC
upper sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G126860_T01 (Zea mays), 3'ss of exon 2
ccttaaatcaggtaaattcatattccataaatgtt--atgaatgtagg-tccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
||| | || | || |||| || | | |||||| | | | | | || | || | | |||| | | ||| || || |||| | ||||| ||||| || ||||||||||||||||||||||| || || | || |||| |||||| |||||||||| |||| ||||||||| || ||
atctaacttgcaattttttagtttacatacttgattggtcaatgtaagataccctactatactttttttcatga-tatttcacaatgttgctttattg--cagTATATCTTCTTCAGATCTGGTTTCAAAGTGGATGGGTGAAAGCGAGAAATTAGTCGCAAATCTTTTCCAAATGGCTCGTGAAAATGCCCCTTCCATTATC
upper sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G27600.1 (Arabidopsis thaliana), 3'ss of exon 2
ccttaaatcaggtaaattcatattccataaatgttatgaatgtaggtccataagtggacatgttcttgc-----aagcatttttaacttttgaattcttca---tcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
| | | || ||| || |||| | | || | | | ||||||| | || || || || ||||| | ||| | |||| || ||||||||||||||||| || |||||||||||||||||||| ||||| || |||||||||||||| ||||| || |||||||| || || || ||
-------ttggttgtttttctatgtca-gtttgtttttacagtgtttatacttggaaacatgttatagcttaagaaaagttgtttcctttttacttcccaaccttcagCGTGTCTTCATCAGACCTTGTCTCGAAGTGGATGGGTGAAAGTGAGAAGCTAGTATCAAACCTTTTCGAGATGGCCCGTGAAAGTGCTCCCTCGATTATT
upper sequence: GLYMA13G39410.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv06s0080g00160.t01 (Vitis vinifera), 3'ss of exon 2
--------------ccttaaatcaggtaaattcatattccataaatgtt-atgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
| | ||| || | ||| | ||||| |||| |||| | |||||| | || || | |||| || ||||| |||||| ||||| |||||||| |||||||||||||||||||||||||||||| | |||||||| ||||| |||||||||| || ||||| ||||| |||||
aagtctgtttctgtttctggttatcgtatttttctcctccttttatgttcatgagcttaggccaataagttggcaagtgcc-------------aactgctg--ttcttttgcagTGTCTCTTCTTCAGACCTGGTTTCAAAGTGGATGGGTGAAAGTGAAAAGTTAGTTTCAAATCTTTTTCAAATGGCTCGGGAGAGTGCTCCTTCCATCATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
ttttaac putative branch site (score: 2)
ttcttcatc putative PPT
atttttaacttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccttaaatcaggtaaattcatattccataaatgttatgaatgtaggtccataagtggacatgttcttgcaagcatttttaacttttgaattcttcatcagTGTTTCTTCATCAGACCTTGTTTCAAAGTGGATGGGTGAAAGTGAAAAGCTGGTTTCAAACCTTTTCGAAATGGCTCGAGAAAGTGCCCCTTCTATCATA
- - - - - - - - - - - - - - - - - - -gaatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caagcat