Sequence
atgc intronic sequence ATGC exonic sequencegtaagataataatataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
Basic information
species | Glycine max |
transcript | GLYMA05G08110.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g42260.2 (Oryza sativa), 3'ss of exon 2
gtaag-ataataatataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttt-tggccgcatgctcc----agCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
||| | || | | | | | | | | | | | | | | | | | || | || | ||||| || | | || | | ||| || ||||| ||||||||||||||||||||||||||||| || || ||||| || | || || | | |||| ||||||| |||| | || | |||
gtatgtatttcccagcaagttgagtgaagctatttgtgtcatgagttttgctacaattttttaccttttgttagtaaaggatgtcgcgaactttctgaactcttgtttcttgcagCGATTGATGCTCCTGGTGGTTTTCTTTTTGAGTGGTGGTCAGTTTTTTGGGATATTTTCATAGCAAGGACAAATGAGAAGCATTCAGATGTTGCGGCTTC
upper sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g42270.1 (Oryza sativa), 3'ss of exon 2
gtaagataataat-ataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaat-ttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
| || | || | | | | | | | | |||| || | || ||| || | | | || ||||| | || | || || ||| | ||| || ||||| |||||||| |||||||||||||||||||| | || ||||| |||| || || | ||| | | || | || | ||| ||
--taattagtgattggaagttgctatggagttatttaatttggcttgtgtt--tgccacaattttaatgatattacttactt----ccttgaattaactttcatac---agCAATTGATGCTCCTGGTGGCTTTCTTTTTGAGTGGTGGTCAATATTTTGGGATATATTCATAGCACAAACAGATCGGGAACATTCTGATGTTGCAACGTC
upper sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g08190.2 (Oryza sativa), 3'ss of exon 2
gtaagataataatataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
| | || || | | | | | | | | | | |||| | | || |||||| | ||||||| || | |||||| ||| || ||||| || || ||||| || || |||||||||||||||||||||||||| | ||||| | | || |||||||| | || | || | |||
ctgatttatgcatgccag-tctctgatgtttctgcattgtaatgaatgcgattttaa----tcttct--tgtactgaaa--gatgtcagcttttgttttgcaaaaaaagCAATTGATGCCCCAGGGGGTTTCCTCTTGGAGTGGTGGTCTGTCTTCTGGGACATCTTCATTGCAAGGACGAACGAGAAGCACTCTGATGTTGCTGCTTC
upper sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G361398_T01 (Zea mays), 3'ss of exon 2
gtaagataataatataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
|| || | || | | | || || | | || | | || || | || ||||| ||| |||| | |||||| ||||| |||||||| ||||| ||||||||||||||||| || ||||| |||| || || | |||| ||||||| |||| | |||| ||
-------------gtacgcctcttgaacagtcacaatggagtctttttagcctgattttatttttgtactgccatggttttgagcttatctttc---------ttgtagCTATTGATGCTCCTGGTGGCTTTCTCTTTGAGTGGTGGTCTGTATTTTGGGATATATTCATAGCAAGAACAAATGAGAAGCATTCAGATGTTGCAGCATC
upper sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G022383_T01 (Zea mays), 3'ss of exon 2
--------------gtaagataataatataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
| ||| | | ||||| | || || | | | | |||| || | || | | || | | || | | | |||| || |||||||| ||||| |||||||| ||||||||||| || |||||||| |||| || || | || ||||||| |||| | |||| ||
gtatgcatttgtctgcaagttgtgtggagttacttttcttttcttgagttcttcc-tgtccgttttgtctgttgcttgtcaagactatt-atttacttcccaaaaactgttcttttttttcagCCATTGATGCACCCGGTGGCTTTCTTTTCGAGTGGTGGTCGGTTTTCTGGGATATATTCATAGCAAGAACTAACGAGAAGCATTCAGATGTTGCAGCCTC
upper sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0016g04550.t01 (Vitis vinifera), 3'ss of exon 2
gtaagataata-atataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
| || | ||| || ||| | ||| || | || | |||||| |||||| | |||| | | | |||| | || | |||| || |||||||||||||| ||||| ||||| ||||||||||| || ||||| |||| ||| || | | |||| |||| ||| | || || || | ||
gcaaaagaatgtatcgaggaatcatta-----aattttcatgagatgtccaaatg----agctcttatcatttgattggtattgattttatgtctgaat-tgaatttcagCCATCGATGCACCTGGTGGCTTTCTCTTTGAATGGTGGTCTGTTTTTTGGGATATATTTATAGCTAGGACAAATGAGAAACACTCGGAGGCTGCTGCATC
upper sequence: GLYMA05G08110.1 (Glycine max), 3'ss of exon 2
lower sequence: EFJ36173 (Selaginella moellendorffii), 3'ss of exon 2
gtaagataataatataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
|| ||| | | | | || || | | | | ||||| | | ||| ||||| |||| | | |||| || ||||| |||||||||||| | || ||||||||||| || ||||||||||| | ||||| ||| | |||||| |||| | || | |||
-----------gtaagagctcctctccgtagagattcttgtcctcataggagttccattgctccttt-----------ttttcccttttttttt-------cgatgcagCGATTGATGCTCCTGGTGGTTTTTTGTTCGAGTGGTGGTCCGTGTTCTGGGACATTTTCATTGCTCGTACGAATGAAAAGCACTCAGAGGTGGCTGCTTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.caactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
taatttactgaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagataataatataggcttttttaggggaaagaaattaggtatatgcaaatgcaactgctcttctaatttactgaatttgacctttacttttggccgcatgctccagCTATAGATGCACCTGGTGGTTTTCTTTTTGAGTGGTGGTCTGTCTTCTGGGACATATATATTGCCATGGTAAATCAGAAGCACCCAGAAGCAGCAGTTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC