Sequence
atgc intronic sequence ATGC exonic sequencegtaagggtgtttcttaaaccaataaaatcttcctaattgcttattatagatgcctgattaatatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
Basic information
species | Glycine max |
transcript | GLYMA01G01230.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA01G01230.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os01g54119.1 (Oryza sativa), 3'ss of exon 5
---------gtaagggtgtttcttaaaccaataaaatcttcctaattgcttattatagatgcctgattaatatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
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gtaagagcagtataagtttgaccctgcctgttatctatgttgtggctagttcatatgctgacttgtagatttatttgttactaccaatagGTCTGCGCTGGACTTTCATCCCGCCTCCAGGAGTATAAATCTGAGAATGCACAGCTGGAGGAACTTCTTGTTCAGGAG
upper sequence: GLYMA01G01230.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G055219_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------gtaagggtgtttcttaaaccaataaaatcttcctaattgcttattatagatgcctgattaat-atttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
|| ||||| || | | | || || | | || || | | ||| | | | | | |||| ||||||||| | |||||||| || ||||| || || ||||||||||||||| ||||||||||||| | ||||
gtaaggataagcataagctcaattgcctcacaactcacactcgatctatgttggttagctctgtttttttgttcgtt----tgttttcaacttaccaacatgttcttttgcccatttgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCCGCCTCCAAGAGTATAAGTCTGAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAG
upper sequence: GLYMA01G01230.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM5G870802_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------gtaagggtgtttcttaaaccaataaaatcttcctaattgcttattatagatgcctgattaa-tatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG------
|| || || || | | || || | || | || | | ||| | | | | | |||| ||||||||| | |||||| | || ||||| || || ||| ||||||||||| ||||||||||||| | ||||
gtaaggataagcataagctcaattgcctcacaactcacacttgatctatgttggttagctctgttttttttttgttcgtttgttttcaacctaccaacatgtttttttgcccatctgttttcaacttacgaatagGTTTGTGCTGGACTTTCATCCTGCCTCCAAGAGTATAAGTCTAAAAATGCACAGCTGGAGGAACTTCTTGTTCAAGAGGTCTAG
upper sequence: GLYMA01G01230.1 (Glycine max), 3'ss of exon 7
lower sequence: AT2G19950.1 (Arabidopsis thaliana), 3'ss of exon 5
--------------------------------------------gtaagggtgtttcttaaaccaataaaatcttcctaattgcttattatagatgcctgattaatatttcctaatgatgctc-agGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
||| | | | | | || | ||| | | | ||||| | | | | || | || | ||| |||| ||||||||| | || ||||||||||||||| ||| | ||||||||||||||||| || ||||||||| |||||
gtaagctcaaatatccattgctactttcctgcatcaaatttgtgataaagtactctttcatgcctgtggttggttctgagcaacct----cagatgtatccattttttgtcttcattttcctctagGTTTGTGCTGGACTTTCGTCCCGTCTTCAAGAAATTAAAGCGGAAAATGCACAGTTGGAAGAGCTTCTCACTGCAGAG
upper sequence: GLYMA01G01230.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv11s0016g03230.t01 (Vitis vinifera), 3'ss of exon 5
-------------gtaagggtgtttcttaaaccaataaaat--cttcctaattgctta---ttatagatgcctga-ttaatatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
||| | ||| | | ||| ||| ||| || || || || | || || ||||| | ||| |||| |||||| ||||||||| | | | ||||||||||||||| |||||||||||||||||||||||| |||||||||||| |||||
ttatggcttctatataatcatattttcttatttgatagaattccttgtcaaatgttttgccttttggaagcaaatcttaatgcatgctattgatattcagGTTTGTGCTGGACTTTTAACCCGTCTTCAAGAATGCAAATCTGAAAATGCACAGTTGGAAGAACTTCTCACTGCAGAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcttcctaattgcttattatagatgcctgattaatatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
tcctaat putative branch site (score: 2)
attaatatttcctaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagggtgtttcttaaaccaataaaatcttcctaattgcttattatagatgcctgattaatatttcctaatgatgctcagGTCTGTGCTGGATTGTCATCCCGTCTTCAAGAATACAAATCTGAAAATGCACAGTTGGAGGAACTTCTCACTTCAGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA