Sequence
atgc intronic sequence ATGC exonic sequence...ttagacttgtgtgtagaatatacagtaaatcaaaagttcttccacatcttatgtgttctcttttcttaatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
Basic information
species | Glycine max |
transcript | GLYMA14G29780.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G004040_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------------ttaga--cttgtgtgtagaatatacagtaaat-caaaagttcttccaca-tcttatgtgttctcttttc------ttaatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
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gtatctgagtacgcttcataaagtacttggtgcaagaagagtatcttggtccattttgggttactacatgaactttattagtgttttccttctgcaccatactgtctttattgctgttgtttgacagtaatgtgatttctcagtacagaaaacaaatacatattcaaatgcttctatgctgtttcagAATGTCAAGACATTTAAAGATGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAAGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCC
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G156069_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------------ttagacttgtgtgtagaatatacagtaa-atcaaaagttcttccacatcttatgtgttctcttttctta----------atctttctctatcaca-ctttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
||| ||| | | ||| || || | | || | ||||| | ||| | | | | || | | | | | || |||||||| || || ||||| ||||| |||||||||||||||||||| | ||||||||||| || || ||||| || || || || || ||||| || ||||
gtatctgattacgcttcataaaatacttgatacaagagtatcttggtccactttgggttactacaaaaacattattagtgtttttctttcgcacaatactgtcttctggttgtctgttagtaatgtgatttctcggtacagaaaacaaatacatattcaaatgataattctatggttttacagAATGTCAAGACATTTAAAGATGTCAAAGGTTGTGATGATGCAAAAAAGGAACTTGAGGAGGTAGTTGAGTATCTCAAGAACCCTTCAAAGTTCACTCGCC
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G53170.1 (Arabidopsis thaliana), 3'ss of exon 5
---ttagacttgtgtgtagaatatacagtaaatcaaaagttcttccacatcttatgtgttc---tcttttcttaatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
| | || ||| | | || | | | | | | | || | | || |||| ||| || |||| || ||| || ||||||||| ||||| |||||||| || || ||||||||||||||||| ||||| || || || || || || || || ||||||||||| |||||||| ||||
attcaatagttctgttcgtgttgcccttgaagccgatatatttataagagctgctccaattgtgtcatttcctaacaatt----atcaagtttacttgcc--gcagAATGTCAAAACATTTAAGGACGTAAAGGGTTGTGATGATGCAAAACAAGAGCTCGAAGAGGTAGTTGAATATCTCAAAAATCCATCAAAGTTTACCCGCC
upper sequence: GLYMA14G29780.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv16s0050g02630.t01 (Vitis vinifera), 3'ss of exon 5
-----------------------------------------------------------------------------------------ttagacttgtgtgtagaatatacagtaaatcaaaagttcttccacatcttatgtgttctcttttct-taatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
||||| |||| | | ||| | ||| || | ||| | | | | || | || ||||||| | || | || |||||||||| || || ||||||||||||||||| |||||||||||||| || || ||||||||||| ||||||||||| ||||| || | |||||||| | |
gtagatatctgatgttacgtgttttgtattatatgttttaagagtgtttctggagatttcaagtctattgagcaagttgtgcaagtgatttagagttgtattcatttcatatggaccatcctgttttttgaagcatgccagttaattgtagtcctgttatttttctctga-gtagttgcctttgctgcagAATGTTAAGACATTTAAGGATGTGAAAGGCTGTGATGATGCAAAACAGGAGCTTGAGGAAGTAGTGGAGTACCTCAAAAACCCTGCAAAGTTTACTAGAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttatgtgttctcttttcttaatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
tcttaat putative branch site (score: 3)
ttctcttttcttaatc CT-rich tract
ttttcttaatcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttagacttgtgtgtagaatatacagtaaatcaaaagttcttccacatcttatgtgttctcttttcttaatctttctctatcacactttctttccttgcagAATGTAAAAACCTTTAAGGATGTGAAAGGTTGTGATGATGCAAAGCAAGAACTTGAGGAAGTTGTGGAGTACCTAAAAAATCCATCTAAGTTTACACGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - -tgtgtgt
- - - - - - - - - - - - - - - - - - - - -ccacatc