Sequence
atgc intronic sequence ATGC exonic sequence...tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcattaataattgatatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
Basic information
species | Glycine max |
transcript | GLYMA15G22520.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g23440.1 (Oryza sativa), 3'ss of exon 6
tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaatt-ctaacactcattaataattgat----atagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
|| | | |||| | | | | | | | || || | |||| || |||| | || || | |||| || |||||||| || || ||||||||||| || ||||| ||||||||||||||||||||||||||||| |||||||| ||||| |||||||| ||||| ||| |
-----aatgttggtaatacttttagagcttgctttgattttgttcattgctgcctataaaaacttgaccgcgattgttttgatgttcattttttatgatccatagGGTGGTGGGCCATACTATCTCATTGGGCGTGCGCTTGGTCCTGAAGTTGGAGTTAGCATTGGACTATGCTTCTTCCTTGGAAATGCAGTTGCTGGATCCA
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g19850.1 (Oryza sativa), 3'ss of exon 4
-tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcattaataattgatatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| | | || | | | || ||| | |||| | | | || | | | | | || | | | || | | || | ||||||| || |||||||||||||| ||| | || |||||||| |||||||||||||| ||||| | || || ||||| || ||||| |||||||||||
gatgatgtatagcatatccaccaagaaccaccatataaattaacctttccaccttgctca-actacaaatggactgactcatctttctttttgaccctcagGGTGGTGGCCCTTACTATCTCATTGGCAGGGCACTTGGTCCGGAAGTTGGAGTTAGTATTGGATTGTGTTTCTTCCTTGGGAATGCAGTTGCCGGAGCTA
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G432083_T01 (Zea mays), 3'ss of exon 3
-------tttgtaaaaaga-aaagcagttttttccccccaaaaaaatctaattctaacactcattaataattgatatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| | || |||| | ||||| | | | || | || || | ||| | | | | | || | || ||| || |||||||| || || || ||||| ||||||||||| ||||||||||||||||||||||| || || ||||||| ||||| || ||||| || || ||| |
tcttgattcaatgctgggacaaagtactttttgttgttctagtg--ttcaa--ccaaaacaaactaacg-ccaacaaact---gacttgcatgttgaatgacctatagGGTGGTGGGCCATATTATCTTATAGGCCGTGCACTTGGTCCTGAAGTTGGAGTTAGTATAGGATTATGCTTCTTCCTCGGGAATGCAGTGGCTGGATCCA
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv10s0003g04530.t01 (Vitis vinifera), 3'ss of exon 5
tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcatt----aataattgatat-agtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| || ||||| | | | || | | || | ||||||||| | | || | | || | | || | | ||||||||||| || || |||||||| || |||||||||||||| |||||||||||||||||||| ||||| || ||||| || ||||| || || ||| | |
----ctttcataactcttgttttactggcttaggcttccttctttttgttgtcctttttgtattaattgataccaatctattttcttgacatctttg-tttctagGGTGGGGGGCCATATTATCTCATTGGTCGTGCCCTTGGTCCAGAAGTTGGAGTTAGCATTGGACTATGTTTCTTCCTTGGGAATGCAGTAGCTGGATCTC
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S22_329V6.1 (Physcomitrella patens), 3'ss of exon 5
------------------------------------------------------------------------------------------------tttgtaaaaagaaaagcagttttttccccccaaaaaaat-ctaattctaacactcattaataattg-atatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
||| | | || | | | | || | | | | | | | | |||| || ||| | ||| || |||||||||| || |||||||| ||||| || || ||||||||||| ||||| || || || || || || || ||||||||||| |||||||| |||||
gttggtttttgttttctaaaagcatttgcataccatcgtgtttgattgagactttgtctttaaatccacatgtttgatctagtagtacgtagtgcagttgaggtcaatgagattgtaccaacttcttgactgctttctggacatttcgatttcgagtgaaggtacatagcaactaggttaactgt-tgtgcaatgcagGGTGGGGGTCCATACTATCTGATAGGACGGGCACTTGGTCCTGAGGTTGGCGTGAGTATCGGACTCTGTTTCTTCCTGGGAAACGCTGTTGCTGGAGCTA
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S139_48V6.1 (Physcomitrella patens), 3'ss of exon 5
----------------------------------------------------------------------------------------------tttgtaaaaagaaaagcagttttttccccccaaaaaaat-ctaattctaacactcattaataattgatat-agtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
|||| | || | || | || | | || | | | | | || | | || || | | ||| ||| | | |||||||||| |||||||| || ||||| || || ||||||||||| ||||| || || |||||||| || || ||||| ||||| ||||| || | |||
gtttgttgtcgtttcctaagcatttacgaattaacacgcttgattgagactgtattttatagtggaagtggttgatctaataatacacaatgcatttgaggtcaataatattgcacttactgcctggccacttgctcacattgctatttggaaggaagttacatcagaatggaattaa--tgtttccttaattcagGGTGGGGGTCCTTACTACCTGATAGGACGGGCACTTGGTCCTGAGGTTGGTGTGAGTATTGGTCTCTGTTTCTTCCTTGGAAACGCTGTGGCTGCCGCAA
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S14_51V6.1 (Physcomitrella patens), 3'ss of exon 5
-----tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcattaataatt--gatatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
| ||| | | | | | | || || | | || | || | |||| | || | |||| | || ||||||| || ||||||||||| |||||| | || || |||||||| ||||| || |||||||| || |||||||| || || |||||||| || ||| |
tgtggtctgtttatggtgttgtaacatgg----ctcatgaagctttgtttaaagtttgaatccaaaatttcagtttaaaacaacgcattctgctacg---gttgcagGGTGGAGGTCCTTACTATCTGATAGGCAGGGCGCTGGGTCCTGAGGTTGGGGTCAGCATTGGACTTTGCTTTTTTCTCGGCAATGCTGTGGCTGGATCTT
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ23975 (Selaginella moellendorffii), 3'ss of exon 3
tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcattaataattgatatagtttagtattttcttgtgta-tgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
||| || | ||| | ||||| ||| || | | || | | |||||||| ||||| || ||||| || || || || |||||||| ||||| || |||| ||||| || ||||||||||| |||||||| ||||| ||| |||
------------------------------------------gttcaaaattttgc-----gttgcgacagtttttcttttggttaagcactggtttatagGGTGGCGGACCGTATTATCTGATTGGTCGAGCTCTTGGTCCGGAAGTCGGTATTAGTATTGGGCTTTGCTTTTTCCTTGGAAATGCGGTTGCTGGATCAC
upper sequence: GLYMA15G22520.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ21598 (Selaginella moellendorffii), 3'ss of exon 3
tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcattaataattgatatagtttagtattttcttgtgta-tgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
||| || | ||| | ||||| ||| || | | |||| | |||||||| ||||| || ||||| || || || || |||||||| ||||| || |||| ||||| || ||||||||||| |||||||| ||||| ||| |||
------------------------------------------gttcgaaattttgc-----gttgcgacagtttttcttttggttaagcactgctttatagGGTGGCGGACCGTATTATCTGATTGGTCGAGCTCTTGGTCCGGAAGTCGGTATTAGTATTGGGCTTTGCTTTTTCCTTGGAAATGCGGTTGCTGGATCAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaacactcattaataattgatatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
attaataattgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtaaaaagaaaagcagttttttccccccaaaaaaatctaattctaacactcattaataattgatatagtttagtattttcttgtgtatgctctgtagGGTGGGGGACCTTACTATCTCATAGGCCGTGCCCTTGGTCCTGAAGTTGGAGTTAGCATTGGTCTATGCTTTTTCCTGGGAAATGCTGTTGCCGGAGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - aagaaaa
- - - - - - - - - - - -ttccccc
- - - - - - - - - - - - - - - -aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - -ctaacac