Sequence
atgc intronic sequence ATGC exonic sequencegtaattgtctttagttaaattggtcaatcatagatagcttttggcattctcctagtcctgattgtacattttggctcttctctcttcatagTTGAAATATCACGAGACTGGAAGGGAGAAAGAATACCTGCCACAAGTTGGTCAATGGAACATGATGAACAAG
Basic information
species | Glycine max |
transcript | GLYMA17G12850.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 9
gtaattgtctttagttaaattggtcaatcatagatagcttttggcattctcctagtcctgattgtacattttggctcttctctcttcatagTTGAAATATCACGAGACTGGAAGGGAGAAAGAATACCTGCCACAAGTTGGTCAATGGAACATGATGAACAAG
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-------gtatgatttgcctttgttaatctcag-tagttggctaactgctctcagctaataatttgggtatgaaattttgtggcttt-cagCTGAAATATCATGATACTGGGAAGGAAAAGGAGTGCTTGCCACAAGTTGGTCAGTGGAACATGGTGAACAAG
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv11s0016g04620.t01 (Vitis vinifera), 3'ss of exon 9
gtaattgtctttagttaaattggtcaatcatagatagcttttggcattctcctagtcctgattgtacattttggctcttctctcttcatagTTGAAATATCACGAGACTGGAAGGGAGAAAGAATACCTGCCACAAGTTGGTCAATGGAACATGATGAACAAG
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gtaat-gtttaacatccccttttctcttattggata--ttttaacatggtc-tgatctaaaatttgt-tcctctattttgttccttgatagCTTAAATATCACGATACCGGAAAAGAAAAAGAATATTTGCCGCAAGTTGGTCAATGGAATATGACAAACAAG
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S173_134V6.1 (Physcomitrella patens), 3'ss of exon 8
---------------------------------------------------------------gtaattgtctttagttaaattggtcaatcatagatagctt--ttggcat---tctcctagtcctgattgtac---attttg----gctcttctctcttcat--agTTGAAATATCACGAGACTGGAAGGGAGAAAGAATACCTGCCACAAGTTGGTCAATGGAACATGATGAACAAG
| |||| || ||| || | | | || | | ||||| | | | | || | | || |||||| | ||| | || || || |||| || || || || |||||||| ||||| | ||| ||||||||||| || ||||||||||||||||||
gtaagtctctctctcttcttcttcttcttcttttttttttttttttttttttttttttttttttttgttgtgttgagt-ggcttacgaagtggcacgtacttgcatgggcatatttgttcgattcttagccgcactatattttgttgggttctgtcttgttgatgcagCTGAAGTACCATGATACCGGAAGGGAAAAAGAGTGCCTTCCACAAGTTGGGCAGTGGAACATGATGAACAAG
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ15357 (Selaginella moellendorffii), 3'ss of exon 10
gtaattgtctttagttaaattggtcaatcatagatagcttttggcattctcctagtcctgattgtacattttggctcttctctcttc--atagTTGAAATATCACGAGACTGGAAGGGAGAAAGAATACCTGCCACAAGTTGGTCAATGGAACATGATGAACAAG
| ||| | ||| || ||| ||||| | ||| | ||||||| ||||| || |||||| |||||||||| | ||| || |||||||| || ||||| ||||||||||||
-----------------------------------------gtatgtcttccgaa----gatcgttaattcaagctctaacgttttctgacagTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG
upper sequence: GLYMA17G12850.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ24991 (Selaginella moellendorffii), 3'ss of exon 10
gtaattgtctttagttaaattggtcaatcatagatagcttttggcattctcctagtcctgattgtacattttggctcttctctcttc--atagTTGAAATATCACGAGACTGGAAGGGAGAAAGAATACCTGCCACAAGTTGGTCAATGGAACATGATGAACAAG
| ||| | || || ||| |||| | ||| | ||||||| ||||| || |||||| |||||||||| | ||| || |||||||| || ||||| ||||||||||||
-----------------------------------------gtatgtcttccgaa----gaccgttaattcaagctcaaacgttttctgacagTTGAAGTATCATGATACTGGACGGGAGAAAGACTGCCTTCCTCAAGTTGGGCAGTGGAATATGATGAACAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttttggcattctcctagtcctgattgtacattttggctcttctctcttcatagTTGAAATATCACGAGACTGGAAGGGAGAAAGAATACCTGCCACAAGTTGGTCAATGGAACATGATGAACAAG
tcctgat putative branch site (score: 3)
cattttggctcttctc putative PPT
tacatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgtctttagttaaattggtcaatcatagatagcttttggcattctcctagtcctgattgtacattttggctcttctctcttcatagTTGAAATATCACGAGACTGGAAGGGAGAAAGAATACCTGCCACAAGTTGGTCAATGGAACATGATGAACAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA