Sequence
atgc intronic sequence ATGC exonic sequence...tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
Basic information
| species | Glycine max |
| transcript | GLYMA09G41330.2 |
| intron # | 5 |
| splice site | 3' |
| intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g45410.1 (Oryza sativa), 3'ss of exon 6
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
| | || | | | | ||| ||| || | | | | || | || | ||| | | | | | || || || ||||||| |||||||||||||||||||||||||||||||| || || || || | || ||||| ||||| ||||| ||||||||||||||||||
gtaactatttcaagcttgcttgattttcatctgtgcatgtgcctac--caaatacattctgtaattgtacctaactgtttaactcattgcactataccagGATTTCAAGATTCAGAACATTGTTGGCTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os12g39070.1 (Oryza sativa), 3'ss of exon 5
-------tttaaggttcaac--atctccaaaaattttatcagttgttttccactct-acagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
||| ||| | | || | || | | || || | ||| | | | || |||| | |||| | ||| | ||| | |||| || |||||||||||||||||||| ||||||||||| || || || || | || ||||| ||||| ||||| ||||||||||||||||||
gtaactatttcaggcttgattaattttca----tctgtgcaaatgcctaccattttcattctgtaagattgtacctaaatgtttaactcatttgcactatacc-----agGACTTCAAGATTCAGAACATTGTTGGTTCTTGTGATGTTAAATTTCCAATCAGGCTGGAGGGACTTGCATATTCTCATGGTGCTTTCTCAAGT
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g29660.2 (Oryza sativa), 3'ss of exon 3
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
|| | | | | |||| || || | | || || | || || | | | || | ||||||| ||||| |||||||||||||| || ||||||||||| || || ||||| || ||||| ||||| ||||| ||||| || ||||| |||
--------gtaatgccactctagctcacatcaattcattcagatt-------gattgtccttgcttat--atcagcttgacgcattggaacatgatgcagGATTTCAAGATCCAGAACATTGTTGGTTCATGTGATGTCAAATTTCCTATTCGCCTGGAGGGCCTTGCTTATTCTCATGGCGCATTCTCTAGT
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G161418_T05 (Zea mays), 3'ss of exon 6
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
||| | | || | || | | ||| | || | | || | ||| || || || | | |||| ||||||||||||||||||| |||||||||||||||||||||||||| || ||| | |||||||| ||||| ||||| |||||||| |||||||||
--------gtaactttttcatac-ttgtgtacattgacctgttctttg----aacaatatgtac------atcagttgctaagttgctgttctaagccagGATTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTCAAGTTTCCAATTAGGCTTGAGGGCCTTGCATATTCTCATGGTGCCTTCTCAAGT
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149238_T04 (Zea mays), 3'ss of exon 5
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
| ||||| | | || | | ||| || | | | || | || | | |||| |||| |||||||||||||| |||||||||||||||||||| ||||| || ||| | |||||||| ||||||||||| |||||||| |||||||||
-----------------gtagctattttcatactcgtgtacagatctg-agctttgaacaat--ttgtacatcagtcactaagttgctgttctatgccagGACTTTAAGATTCAGAATATTGTTGGCTCTTGTGATGTAAAGTTTCCAATTAGGCTTGAGGGCCTTGCCTATTCTCATGGTGCCTTCTCAAGT
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: AT3G13445.1 (Arabidopsis thaliana), 3'ss of exon 6
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
|| ||| ||| ||| |||| | | | || | | |||| | | | | | | || | || |||| ||||||| ||||||||||| ||||| || |||||||||||||| ||||| || ||||||| |||||||| || || || | |||||||||||||
------gtacaatttctttaaaccttttccc---tatccaacattttttttcttacttttgcttatactaaatatattcaattgttacatcctgc---agGATTTCAAGATTCAGAATATTGTAGGTTCTTGTGATGTCAAATTCCCTATAAGACTTGAAGGTCTTGCTTACTCTCACGCTGCTTTCTCAAGT
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: AT1G55520.1 (Arabidopsis thaliana), 3'ss of exon 6
----------------------------------------------tttaaggttcaacatctccaaaaattt-tatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
|| | || | | ||| |||| | | || || || | | | || | ||| | | | | | ||| ||| ||||||||||||| ||||||||||| ||||| ||||||||||| ||||||||| | ||||| |||||||| || || ||| ||||||||||||||
gtactcatatgtctctctctggtcctgatccagcacacactgtgttattcatttttatctcaatcaacaattcgtgtgtatttttatcggaaggaaaaattacgtataaagtctagtaataaaattgctgattacattttgc---agGATTTTAAGATACAGAACATTGTAGGCTCATGTGATGTCAAATTCCCCATTAGGCTTGAAGGTCTTGCATACTCTCATAGTGCTTTCTCAAGT
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0004g00180.t01 (Vitis vinifera), 3'ss of exon 6
---------------------------tttaaggttcaac-atctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
| | | | | | | | | || ||| | | | | | | ||| | | | | | | |||| | | | | | ||||||||||||||||||||||| |||||||| |||||||| || |||||||| | ||||| || ||||| ||||| |||||||| || || ||
gtatttattccattacatctctctctctctgtgatgtagccaatttctgttatgctatt--cttctccttgtttttttgccactgttcttattttatattgactgctgttttttattgtgggatgtagGATTTTAAGATTCAGAACATAGTTGGCTCCTGTGATGTTAAATTCCCCATAAGGCTTGAAGGCCTTGCATATTCTCATGGTGCCTTTTCCAGC
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ36040 (Selaginella moellendorffii), 3'ss of exon 5
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
|| | || || || |||||||| | | | | | | | ||||||||||||| ||||||||||||||||| ||||| || |||||||| || || | ||||| || || || | || ||| ||||||||
-----------------------------------gtatgaag----acgaaaacacattgtggtc-tgagctcaaacttagtaacgtccgtgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGTGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC
upper sequence: GLYMA09G41330.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ04980 (Selaginella moellendorffii), 3'ss of exon 5
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaag-cagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
| |||| || |||||||| | | | | | | | ||||||||||||| ||||||||||||||||| || || || |||||||| || || | ||||| || || || | || ||| ||||||||
----------------------------------------gtatgaagaagaaaacacattgtggtc-tgagctcaaacttagtaacgtccatgatcgcagGATTTTAAGATCCAGAACATTGTTGGCTCCTGCGACGTTAAGTTCCCGATCAGATTGGAGGGCCTGGCGTACGCTCACGGTCACTTCTCAAGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
cattgat putative branch site (score: 4)
tttattcctttttctt CT-rich tract
atttattcctttttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttaaggttcaacatctccaaaaattttatcagttgttttccactctacagaagcagtttgtggtcattgatttattcctttttctttattctgctttagGATTTTAAGATTCAGAACATTGTTGGCTCTTGTGATGTCAAGTTCCCCATTCGACTTGAGGGTCTTGCCTATTCCCATGGTGCTTTCTCAAGT
- - - - - - - -ctccaaa
- - - - - - - - - - - - - - - - - - - - ccactct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - gtttgtg
