Sequence
atgc intronic sequence ATGC exonic sequence...acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacctctcacttagtatgtatattctgtgccttgtatttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
Basic information
species | Glycine max |
transcript | GLYMA12G02500.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g44230.1 (Oryza sativa), 3'ss of exon 3
--------------------------------------------------acatttctggttgcatgagtcagt-agaggcattttagagaagtagcttccacctctcacttagtatgt-atattctgtgccttgtatttcctgtattt-cagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
|||| || || ||| | | | | | | || | | | | |||| ||| | || || || | | |||| ||||| ||||| ||||| |||||||| |||||||||||||||||||| ||||| || ||||| || ||||||
gtaagcttgtatatgtgctcaacgttggaactgcataatgatttttgtctcagtttcaggcaaaatatatcatttattttcctctgtaataactttgtaaaagcgaaaacttctgttgtcagatgttgctaattacaaaggcaaaattttcagGTTCGCAAATTCAGTAAACATTGCAGAAGTTGTGATAAATGTGTGGATGGTTTTGATCATCACTGTCGG
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g38970.1 (Oryza sativa), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacc--tctcacttagtatgtatattctgtgccttgtatttc----ctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| || | | || | | || | | | | || || | || | | | | || | ||||| | | | | | ||||| ||||| ||||| ||||| || ||||||||||| |||||||||||||| || ||||| |||||||||
--------------gtatgttgatcta--tcttctggggatgcatcattcagtaaacttatttgatttttgtgttataactcttgttatacaaaattatttggcagGTTCGCAAATTCAGTAAACACTGCAGAAGTTGTGACAAATGTGTTGATGGATTTGATCATCATTGTCGG
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G321767_T01 (Zea mays), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacctctcacttagtatgtatattctgtgccttgtatttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| ||| | || || | || | ||| | | || | | ||| || | | | | |||||| ||||| ||||||||||| || || |||||||| || ||||| ||||| || ||||| |||||||||
--------------gtatgtcgatttagcttttc------accaggcttcactatctagcttgtgttgttcatctttgtttcacaaaagtaatttctcagGTTCGCAAATTCAGCAAACACTGCAGGAGTTGTGACAAGTGTGTGGATGGATTTGATCATCATTGTCGG
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G149442_T01 (Zea mays), 3'ss of exon 3
-------acatttctggttgca-tgagtcagtagaggcattt--tagagaagtagcttccacctctcacttagtatgtatattctgtgccttgtattt------cctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
|| |||||| | || | | ||| || || || || | | || |||| ||| | || | | ||| | |||||||| ||||| ||||| ||||| || ||||||||||| || ||||| ||||| || ||||| || ||||||
gtacgttctgttcaacgttgcaaccatgtagcatatttttttcctaagtcagcaggttatatc-ctgtcttaacttgtgttgtcatcacttccaattaagaaagatgatttttcagGTTCGCAAATTCAGTAAACACTGCAGAAGTTGTGACAAGTGTGTGGATGGATTTGATCATCACTGTCGG
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G22180.1 (Arabidopsis thaliana), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacctctcacttagtatgtatattc--tgtgccttgtatttcctgtatttca--gGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
||||| | | | | | |||| | || |||||| | | || || || || |||| | ||| | | ||||| ||| |||||||||||||| |||||| ||||||||||||||||||||||| | || ||||||||||| |
---tttcttggt-ctttatcttctagaatctgctttaagaagtctttagggaaagcaatttggttcagattttagatgtgtactcaattatgtatgtttcacagGTACGCAAGTTCAGCAAGCATTGTCGAAGTTGTGATAAATGTGTTGATTGTTTTGATCACCATTGCAAG
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv03s0017g01770.t01 (Vitis vinifera), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagctt--ccacctctcacttagtatgtatattctgtgccttgta--tttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| ||||| || | || | | | | | | | || || | | | || | | || | | ||| | || ||||| ||||| ||||||||||| |||||||||||||| |||||||| ||||| || |||||||||||||||
---actttggttatg-atgtagacatgcccacatgcagcttatggtctaacaatatttccttttgggctttttttatttaccaagaaaatttttcatgttgcagGTACGCAAATTCAGCAAACACTGTAGAAGTTGTGACAAATGTGTGGATGGATTTGATCACCATTGTCGG
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S96_102V6.1 (Physcomitrella patens), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattt-tagagaagtagcttccacctctcacttagtatgt-atattctgtgccttgtatttcctgtattt-cagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
|| | | | | || || || | | || || | | | ||| | ||| ||| | | ||| | | || |||| |||| || |||| ||| |||||||| ||||| || || ||||||||||||||||| || ||||||||||||
---gttgtattggtcaatgcttgtgaggggatctctctagcagcaaaatttcttttgtactaaaattgtgatagtaaaaactgtgtttgttctcgatttgtagGTTCGGAAGTACAGTAAACATTGCAGAAGCTGCGACAAATGTGTTGATGGCTTTGACCACCATTGTCGG
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S64_122V6.1 (Physcomitrella patens), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacc--tctcacttagtatgtatattctgtgccttgtatttcctgtattt--cagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
| | ||| | | | ||| || | | || | || ||| | || || | || | | || ||| ||||| |||||||| |||||||||||| |||| || ||||| || || ||||| |||||||| ||||||||
---tcttaaaccccatacataggaatcagcacatttggtactgagtgttgactgatctgtatcaggctg-gtgtttgataatagtgaagaaatggttttgacagGTTCGCAAGTTTAGCAAACATTGTCGAAGCTGCGATAAGTGCGTGGATGGTTTCGATCATCATTGTCGA
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S118_83V6.1 (Physcomitrella patens), 3'ss of exon 3
------------------------------------------------------------acatttctggttgcatgagtcagtaga-ggcattttagagaagtagcttccacctctcact--tagtatgtatattct-----------gtgccttgtatttcc----tgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
|||||| | | | | | ||||| | || | | ||| | | || | | ||| |||| ||| ||| ||| || | || | ||||| ||||| | ||| || |||||||| || || |||||||| |||||||||||||| ||||||||||||
gtaatttgttctaaggattttattattattattattattattattattattattttaaatttatttctagacttctaaaatcttggttagcattat-gatcaattgctccaagctttaatccatagcttgtaaatttgtcaagctaaaagtgatctgttgtttcgtattggacgacagGTTCGCAAATACAGTAAGCATTGTAGGAGCTGCGATAAATGCGTTGATGGCTTCGACCACCATTGTCGG
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ36891 (Selaginella moellendorffii), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacctctcacttagtatgtatattctgtgccttgtatttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
||| |||| | | || || | | | | || | || ||||| | |||||||||||||||||| |||| |||||||| ||||||||||| |||||||||||||||||
-----------------------------------gtttgagttctttccgtgagtatgtcgacattgatttgataagtttggtttatctcacg---cagGTTCATAAGTTCAGCAAACATTGTCGAAGCTGTGATAAGTGTGTTGATGGATTCGATCACCATTGTCGT
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ29393 (Selaginella moellendorffii), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacctctcacttagtatgtatattctgtgccttgtatttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
||| || || | ||||| | | | ||| | || | ||||||||||||||||||| ||||| || || ||||| || || ||||| |||||||| ||||| |||||
-----------------------------------------gtaatcgtcaggacttagc---tatgtgtgcatggcatttaccattgtttctacct-agGTGCGCAAGTTCAGCAAGCATTGCAGGAGCTGTGACAAGTGCGTTGACGGCTTCGACCACCACTGTCGC
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ33542 (Selaginella moellendorffii), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacctctcacttagtatgtatattctgtgccttgtatttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
||| |||| | | || || | | | | || | || ||||| | ||||||||||| |||||| |||| |||||||| ||||||||||| |||||||||||||||||
-----------------------------------gtttgagttctttccgtgagtatgtcgacattgatttgataagtttggtttatctcacg---cagGTTCATAAGTTCAGCAAGCATTGTCGAAGCTGTGATAAGTGTGTTGATGGATTCGATCACCATTGTCGT
upper sequence: GLYMA12G02500.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ12139 (Selaginella moellendorffii), 3'ss of exon 3
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacctctcacttagtatgtatattctgtgccttgtatttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
||| || | | || || || | | || ||| | || | ||||||||||||||||||| ||||| || || ||||| || || ||||| |||||||| ||||| |||||
-----------------------------------------gtaatcgtcaggacgagcaatgtgtgcatggcatttacc----attgtttctacct-agGTGCGCAAGTTCAGCAAGCATTGCAGGAGCTGTGACAAGTGCGTTGACGGCTTCGACCACCACTGTCGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttccacctctcacttagtatgtatattctgtgccttgtatttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
ctctcac putative branch site (score: 3)
tatttcct putative PPT
ttagtatgtatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
acatttctggttgcatgagtcagtagaggcattttagagaagtagcttccacctctcacttagtatgtatattctgtgccttgtatttcctgtatttcagGTGCGCAAGTTCAGCAAACATTGTAGAAGTTGTGATAAATGTGTTGATGGCTTCGATCACCATTGTCGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- -tttctgg
- - - - - -tgcatga
- - - - - - - - - - - - - -ggcattt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tctgtgc