Sequence
atgc intronic sequence ATGC exonic sequence...cattgatgcatgctgaaatttgatgtttttatgctgttctatgagaaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
Basic information
species | Glycine max |
transcript | GLYMA06G07010.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g55260.1 (Oryza sativa), 3'ss of exon 2
------------cattga--tgcatgctgaaattt-----gatgtttttatgctgttc-tatgagaaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
||| | || | ||||| ||| ||| || | || || | || || | | | || || || | | || | ||||| | |||||||| || |||||| |||| |||||||| ||||| || ||| |||| ||||| |||||||| ||||||||||||||||||| | | |
gtaatttcctaatatttacctgttcattaaaattcatagggatcatttgatttcaaccatacaagcagtagtttgattgctaaatgttactcattcttctcttctgtttaatggatgcagTACTTGTCAAATGCGGCACTTGCAAGAACTAGTGTTGCTAGTACTACTGTACTATCTTCAACGTCAGGACTCTTCACTCTTTTCATTGGTGTGCTACTTG
upper sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G882708_T03 (Zea mays), 3'ss of exon 3
---------------------------------------------------------------------------cattgatgcatg---ctgaaatttgatgtttttatgctgttctatgagaaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
| ||| ||| |||||| | ||| || || || || || || | | | | || || || || | |||||| |||| |||||||| |||||| |||| |||||||| ||||| ||||| | || |||||||||||||| ||||||||||||||||||| || | |
gtaaactttgcatgttaatttgtaattcctggggactagaaatgttcatctgaataacatttgtttctcaaaaactactgacatatgttcctgaaagcctagatttcaat-----cataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG
upper sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM5G882708_T01 (Zea mays), 3'ss of exon 1
--cattgatgcatg---ctgaaatttgatgtttttatgctgttctatgagaaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
| ||| ||| |||||| | ||| || || || || || || | | | | || || || || | |||||| |||| |||||||| |||||| |||| |||||||| ||||| ||||| | || |||||||||||||| ||||||||||||||||||| || | |
actactgacatatgttcctgaaagcctagatttcaat-----cataaaagcaatactttgatagttaaaggtaactcatttttctcttatgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACAGTGCTGTCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGTTTTACTTG
upper sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G064831_T02 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------------------cattgatgcatgctgaaatttgatgtttttatgctgttc-tatgagaaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
| |||| ||| | | | | | || || || || || || || | | | | | || || || | || | |||||| |||| |||||||| |||||| |||| |||||||| ||||| || ||| | || ||||||||||| || ||||||||||||||||||| || | |
gtaattttacaatggctttgcatgttaatttgcaattccaggggacttgaaatgttcatgtgaataacttttgacatttgtttctcaaaaactactgatatatgtttcag---aaagcctaaatttcaatcgtaaaagcaatactttgataggtaaaggtaactcatttttctcttacgctgaatgaatgcagTATTTATCGAATGCAGCGCTTGCAAGAACTAGTGTTGCCAGTACCACCGTACTGTCTTCAACTTCAGGGCTCTTCACTCTTTTCATTGGTGTTTTACTTG
upper sequence: GLYMA06G07010.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0008g06500.t01 (Vitis vinifera), 3'ss of exon 2
cattgatgcatgct-gaaatttgatgtttttatgctgttctatgagaaaacttta------gaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
|| | | | ||| || || ||| | || | | ||| || | || ||| || ||| ||| | | |||| || || |||||| | |||||||| || |||||||| ||||||||||| |||||||| || |||| |||||||||||||| ||||||||||||||||||||| || |||
------tgtcttttagggattctattttacaatggtagtccaggttaaagtcctatgtgaaggaattcagagagagtacttgattg-tgattttctattttttgcagTATTTTTCAAATGCTGCACTTGCACGTACAAGTGTTGCTAGTACAACCGTCCTATCTTCAACTTCAGGACTCTTCACTCTTTTCATTGGTGCACTTTTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
tattaat putative branch site (score: 2)
ttttcttctgttgctt CT-rich tract
tttattaattttcttc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cattgatgcatgctgaaatttgatgtttttatgctgttctatgagaaaactttagaaaagcagcagcggtgctttattaattttcttctgttgctttcagTATCTATCAAATGCAGCCCTTGCACGAACAAGTGTTGCAAGTACAACAGTATTATCATCAACTTCAGGACTTTTCACTCTTTTCATTGGTGCATTTATGG
- - - -gcatgct
- - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - -tgctgtt
- - - - - - - - - - - - - - - - - - - ctatgag
- - - - - - - - - - - - - - - - - - - - - - - - - - - gaaaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcagcgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcttta