Sequence
atgc intronic sequence ATGC exonic sequence...atttataatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataagacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
Basic information
species | Glycine max |
transcript | GLYMA12G03490.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g05690.1 (Oryza sativa), 3'ss of exon 3
-atttataatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataagacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
|| ||||| | | | | | | | | || ||| | | |||| | ||| ||||| | | | | ||||||||||||||||||||||||| ||| || ||||||||||| | ||| | ||||| || |||| |||||||| |||||||| || ||||| | ||
tatctataaaacttgggagtagattgattttaaccaaagtcaaaataacttatagtagtagtaattaagaaagtaattaagggatgaaatgcaaatg-cagGGAGATAATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGCTGGCGACGGTGTACGTGCTGACGCTGACGCTGCCGTCGGCGTCGGCG
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g14080.1 (Oryza sativa), 3'ss of exon 5
-atttataatttaagcttttgcaattgtggtgatatgctactaattaattagttt-cgagagtataagacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGC-AGCA
| ||| | | | | ||| || | | ||| || ||||| | | | | || | | | |||| | || | || ||||||||| |||||||||||||||| ||| || ||||||||||| | ||| | |||| || ||||| |||||||| |||||||| || ||||| || |||
cagttaca--tcgatcgtttacagcagcgtcaatactgtaataattgaccaaactgtcaaagcagtttgtgacaacattacgtgtgattttggtgcgcgcagGGAGATCATGCACGCGATGTGGAGGCCGCAGAAGTTCAAGGCGATCTACCTGATGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCGGCGGCGAGC-
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G129413_T01 (Zea mays), 3'ss of exon 1
-atttataatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataagacaaatatattaatgat-acttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
| | | | || || | | | | | || || || | | | | || | | | | ||| | |||||||| ||||||||||||||| ||||| |||||||||||| | ||| | ||||| || ||||| |||||||| ||||| || || || || || ||
tgccaccgacacatgggtcccagcctgccacgaggcacca-tgactcgttgcttccgttgttgtgtgcgcttctttttgacgttgatacatacatatg-tagGGAGATCATGCACGCGATGTGGCGTCCTCAGAAGTTCAAGGCCATCTACCTGCTGGCGACGCTGTACGTGCTGACGCTGACCCTCCCTTCCGCCGCCGCC
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G149481_T04 (Zea mays), 3'ss of exon 4
attta--taatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataagacaaatatattaatg-atacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGC-AGCA
|| | | | ||| || ||||| | | ||| | | || || | |||| || | | | | ||| | || ||||||||| ||||||||||||||| ||| || ||||||||||| | ||| | |||| || ||||| |||||||| |||||||| || ||||| || |||
atcaaagcagtactagcaatt--aattgaaaggtgactggactgaacgaacagcatcaacagtaattagtaatggtttgcacgcatatatatatacacg-cagGGAGATCATGCACGCGATGTGGCGGCCGCAGAAGTTCAAGGCGATCTACCTGATGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCGGCGGCCAGC-
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G045057_T02 (Zea mays), 3'ss of exon 5
--------------------atttataatt-taagcttttgcaattgtggtga----tatgctactaattaatt---agtttcgagagtataagacaaatatattaatg-----atacttgtactggta---acagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
| |||| | || | || | |||| || | ||| | || || | || ||| || | | | | || | | || | ||| ||||||||| ||||||||||||||||| || || ||||||||| | | ||| | |||| || ||||| |||||||| |||||||| || || || | ||
gtaagcctcagctgccagcagtctatatctatacccacacacagcagaagtgaagtttaggtcacttcagagttcagagctacgtacgtacgtgatgagtgtcacagtgtgtgtacaaatgggccggttggtgcagGGAGATCATGCACGCGATGTGGAAACCGCACAAGTTCAAGCTCATCTACCTGGTGGCGACGCTGTACGTGCTGACGCTGACGCTGCCGTCCGCCTCCGCC
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0038g02140.t01 (Vitis vinifera), 3'ss of exon 5
atttataatttaagcttttgcaattgtggtgatatgctactaattaattagt---ttcgagagtataag-acaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
||| || || ||| || || | | || || | ||| |||| ||| | | | | | ||| | || || | | | | | ||| ||||||||||| || |||||||| || || || ||||||||| ||||| | ||||| ||| ||||||||||||||||||| ||||| || || ||||||
ttttgaaa---aacagtttccacttattccaaaattttaattattgtttagaaaattctaaatcaagtgtataaaaacat-aaggttttgatttttttttgcagAGAGATAATGCATGCAATGTGGAAACCACAGAAATTCAAGGCCATATACCTGCTGGCTACCGTGTATGTGCTGACACTGACACTTCCGTCCGCGGCAGCA
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ34222 (Selaginella moellendorffii), 3'ss of exon 5
atttataatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataagacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
|| | ||| || || | | | | | || || | || || | | | | | ||||||||| |||||||||||||||||||| |||||||||||| | || | | || ||| | || || | || |||| || || || || | |||
-------------------------gtaagctttcgcttct--ttcgctgttcttgcatggatc-gataggcatcttctcataaactttgatcttcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA
upper sequence: GLYMA12G03490.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ21839 (Selaginella moellendorffii), 3'ss of exon 5
atttataatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataa-gacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
|||||||| || | | ||| | | || | || ||| | || | | | || | ||| || | ||||||||| |||||||||||||||||||| |||||||||||| | || | | || ||| | || || | || |||| || || || || | |||
---------gtaagctttcgcttcttt-------cgctgttcttgcatggatcgataggctatgttgtcatcttttctcataaactttgatct--tcccagGGAGATCATGCACGCGATGTGGAAGCCCCAAAAGTTCAAGTGGGTCTATCTCGTCGCTACCATCTACGTCTTCACCTTGACACTCCCGTCCGCCACGGCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aattagtttcgagagtataagacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
tattaat putative branch site (score: 2)
tataagacaaatatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttataatttaagcttttgcaattgtggtgatatgctactaattaattagtttcgagagtataagacaaatatattaatgatacttgtactggtaacagGGAGATAATGCACGCGATGTGGAAGCCTCAAAAGTTCAAGGCCTTATACTTACTGGCAACCCTGTATGTGCTGACACTGACGCTTCCATCGGCAGCAGCA
- - - - - - -gcttttg
- - - - - - - - - - - - tgtggtg
- - - - - - - - - - - - - - - - - tgctact
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aagacaaa