Sequence
atgc intronic sequence ATGC exonic sequencegtgttaatggttttcagttgttgtttatataccaaaagacattctcagtttcttggctaaccatagagtccatccttttttgtttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT
Basic information
species | Glycine max |
transcript | GLYMA12G17220.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G17220.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G20650.2 (Arabidopsis thaliana), 3'ss of exon 3
gtgttaatggttttcagttgttgtttatataccaaaagacattctcagtttcttggctaaccatagagtcc---atccttttttgtttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT
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----------------------gttcttgacttaaa--acaatcttattgttcatgtcaattgttatttctcaaaactaatctcattgtaatgcttttaccagGGTGGTGATTTGATCAAGTGGGATAAGGCGAGAATCGGGTACTATGTTGGAATTGATATTGCTGAAGGGTCG----
upper sequence: GLYMA12G17220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv04s0023g02860.t01 (Vitis vinifera), 3'ss of exon 2
gtgttaatggttttcagttgttgtttatataccaaaagacattctcagtttcttggctaaccatagagtccatccttttttgtttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT--------------------------------------------------------------------------------------------------
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--------------------------------------gtgtcctcattcagctttatgctctccgaggggatgctgttcttgattttgctcgtggcaagggtggtgatctaatcaaataggacaaggcaaagattggatactatgttggcaccaatattgctgaaggcttgatagaagACTGTTGTACACGCTATAATGGTGACATAGACCATCATCAAAGGCGCAAAAAGTTCACATTTCCGGCTCGCCTTATATGTGGAGATTATTTTGAG
upper sequence: GLYMA12G17220.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0014g04740.t01 (Vitis vinifera), 3'ss of exon 3
gtgttaatggttttcagttgttgtttatataccaaaagacattctcagtttcttggctaaccatagagtccatccttttttgtttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT
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--------gtgttatagagcttttatatctatcaaattg-agtggcagttctttt----atgctaatattctttcttgttcttcacccttttttcactagGGTGGTGATCTAATCAAATGGGACAAGGCAAAGATTGGATACTATGTTGGCATCGATATTGCTGAAGGCTCG----
upper sequence: GLYMA12G17220.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S49_100V6.1 (Physcomitrella patens), 3'ss of exon 4
----------------------gtgttaatggttttcagttgttgtttatataccaaaaga----cattctcagtttcttgg--ctaaccatagagtccatccttttttg---tttcataatgtttac-cagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT
|| | || | | | ||| | | | | || || |||| || | || | || | | || | | |||| ||| | | | ||||| || ||||| ||||| |||||| |||| |||||| || || ||||||||||||||||| |||||||||
gtgcacagcttctgagattgtcctgcaatatattctttgatcttggtcaaactctaaccgaggcccattttccttgtcataattctgaatacggacagttttcccatttggcatttagctgtaatgatgcagGGGGGAGATCTGATCAAGTGGGACAAGGCGTCAATTGGTTACTACGTTGGTATTGACATTGCCGAAGGCTCG---- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtttcttggctaaccatagagtccatccttttttgtttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT
ggctaac putative branch site (score: 2)
ttttttgtttcataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgttaatggttttcagttgttgtttatataccaaaagacattctcagtttcttggctaaccatagagtccatccttttttgtttcataatgtttaccagGGTGGTGATCTTATCAAATGGGACTAGGCCAAAATTGGATATTATGTTGGTATTGACATTGCTGAAGGCTCGGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG