Sequence
atgc intronic sequence ATGC exonic sequencegtaagttcataacttccttatatttgttatatctttctagagaattgttgtaatgaaacttcaattgaatcgtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
Basic information
species | Glycine max |
transcript | GLYMA07G30990.2 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g36660.1 (Oryza sativa), 3'ss of exon 5
--gtaagttcataacttccttatatttgttatatctttctagagaattgttgtaatgaaacttcaattgaa-------tcgtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
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gtatgattccatatactttactgatcttgtgtaactgttacatgtcttaacata-tagatcttaaattataatccctcttgtagTGTACAAGAAACACTACCCTCCTGCCCTAAAGGATGATGTTTGGAGATTGGAGAAGATTGGAAAGGATGGTGCATTTCACAAGAAGCTAAACTCAAATGG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g08120.1 (Oryza sativa), 3'ss of exon 5
gtaagt--tcataacttccttatatttgttatatctttctagagaattgttgtaatgaaacttcaattgaatcg--tagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
|||||| || || | || || || | | | ||| | | | | | || | | | |||| || ||||| |||||||| ||||| ||||| |||||||||||||| | || ||||| || |||||||| || || || || || || || ||||||||
gtaagtcctctgaagcaaccatgatatgatacgattcttcatgatatttctattaactgtttgaatttcatttgattagTGTATAAGAAGCACTACCCACCTGCGTTGAAAGATGAGGTCTGGAGGTTAGAAAAGATAGGGAAGGATGGATCTTTCCATAAGAGACTGAACAAAGCTGG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 5
----------------gtaagttcataacttcctt---atatttgttatatctttctagagaattgttgtaatgaaactt--caatt--gaatc--gtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
|| || | || | | | ||| | | | | |||||| | || | | ||| | || |||| |||||||| |||||||| ||||| |||| ||||| || |||||| | || ||||||||||||||||| |||| ||||| | | ||||| |||
gtatgtgtgacacactgttgatttactcattagatgaaacaaagattacctgtatttttagaatttgcatcgccaagcatgctgattttgtatttattagTGTACAAGAAGCACTACCCACCTGCGCTGAAGGATGATGTTTGGAGATTAGAAAAGATTGGCAAGGATGGCGCATTCCACAAGAAGTTAAATGCCAGTGG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0181g00220.t01 (Vitis vinifera), 3'ss of exon 6
-----------------gtaagttcataacttccttatatttgt---------------tatatctttctagagaattgttgtaa---tgaaacttcaattgaatcgtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
|| | | || | || ||| | ||| | | ||||| | || || || || | ||||| ||| || || |||||||||||| |||||||| ||||| ||||||||||| || ||| || |||||||||||||||| ||||||||||| ||||| ||| | |||||||||||
gtgagttgatgttcagtgtcaaattattatttacttctttttatatatgcataaatgtgtgtatctgttgggatgatggtggtgaatctgaaagatcatttttttcccagTATACAAGAAGCACTACCCTCCTGCATTGAATGATGAAGTTTGGCGATTGGAGAAGATTGGCAAAGATGGGTCATTCCACAAGAGGTTGAATAAAGCTGG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S84_168V6.1 (Physcomitrella patens), 3'ss of exon 4
--------------------gtaagttcataacttccttatatttgttatatctttctagagaattgttgtaatgaaactt---caattgaatc--gtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
|||| | | || | | | ||| | || |||| | ||| | | | | || | ||| |||||||| |||||||||||| |||||||||||||||||||| || |||| || ||||||||||| || | |||||||| | || ||| | || |
gcctttttacggtccctggaagaagtacgaaggatcagtggaaatattaggaatggatacgtttctgtttctaagaatcgttgtcggtcacattctgcagTTTACAAGAAGCACTACCCGCCTTCCTTGAATGATGAGGTCTGGCGATTGGACAAAATTGGCAAGGACGGTGCTTTTCACAAGCGTCTCAATCAGTCTCG
upper sequence: GLYMA07G30990.2 (Glycine max), 3'ss of exon 3
lower sequence: PP1S21_379V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------gtaagttcataacttccttatatttgt-tatatctttctagagaattgttgtaatgaaacttcaattgaatcgt-----agTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
| | | | || | | || | | || | |||||| | | | | | || | ||| ||||||||||| |||||||| ||| ||| ||||||||| ||| | |||| || ||||||||||| || | |||||||| | || ||| || || |
tgcatttttgttatcacttgaagaagtgtgaacaatttgtggaaatataaaaatgagtataatattgtttctgagcctcgttgttggtctcattctgcagTGTACAAGAAACATTACCCGCCAGCCCTGACTGATGAGGTTTGGCGGTTGGATAAAATTGGCAAGGACGGTGCTTTTCACAAGCGTCTCAATCAATCTCG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatttgttatatctttctagagaattgttgtaatgaaacttcaattgaatcgtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
ttatatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttcataacttccttatatttgttatatctttctagagaattgttgtaatgaaacttcaattgaatcgtagTATACAAGAAACACTACCCGCCTGCCTTGAATGATGAGGTCTGGAGACTGGAGAAGATTGGCAAGGATGGGTCATTTCACAAAAGGCTAAATAAAGCTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG