Sequence
atgc intronic sequence ATGC exonic sequencegttactaccctattattgaaattttcctattcagtaacttttgtggctgtaaggatatccttttttgctgcataaattaattccccaggttgcttggaaaccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
Basic information
species | Glycine max |
transcript | GLYMA18G04990.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G04990.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 9
--gttactaccctattattgaaattttcctatt-cagtaa--cttttgtggctgtaaggatatccttttttgctgcataaattaattccccaggttgcttggaaaccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
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gtgaaaccggcttgtcaaatggctgcacgtacggtggttatccctttttaggaccaacgttaccatgatttggtatg-acatgaaaaatgcatgat-cttgatgac-agGGAACAATTGCACACGCTCTGGAGAAGACAAAGTACGAGGATTCAGATGTTAAGTGGAGAGAGATGGACCAGAAGTACCATTTCTCTTGCCAATTTACCG
upper sequence: GLYMA18G04990.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G060659_T01 (Zea mays), 3'ss of exon 8
gttactaccctattattgaaattttc--ctattcagtaacttttgtggctgtaaggatatccttttttgctgcataaattaattccccaggttgcttggaaaccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
|||| | | | || |||| | | || | | || |||||| ||| || | | | || | | ||||| || ||||| || ||| |||||||||| |||||||||||||||||||| ||||||| ||| | |||| ||||| || ||||| || ||||||| |
---------------gtgaagtgatgggccatcaagtagagtct-tgaaagattgattactttttttt--tgc-tagtatgacacagaagatgatcttattgacagGGGACAATCGCGCACGCTCTAGAGAAGACAAAGTATGAAGATTCAGATGTGAAGTGGAGAGATCTGGATCAGAAGTACCATTTCTCCTGCCAATTCACTG
upper sequence: GLYMA18G04990.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G045171_T01 (Zea mays), 3'ss of exon 3
gttactaccctattattgaaattttcctattcagtaacttttgtggctgtaaggatatccttttttgctgcataaattaattccccaggttgcttggaaaccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
| | ||| | || ||| | | | | ||| || | || ||| || | ||| | | | | ||||| || || || |||||| | |||||||| |||||||| ||||| ||||||||||||| || | || | || |||||| |||||||| || || | |
-----------gtgaaggaacaccttctcttctccttgtgccg-gccggtaccaatcaagtcaaacctgacaaaaaagaaagcacca--tcgatgtaa---cagGGGACGATTGCGCATGCTCTCGAGAAGACAAAGTATGAGGATTCCGATGTCAAGTGGAGGGAAATGGACCACAGGTATCATTTCTCATGCCAGTTTACTG
upper sequence: GLYMA18G04990.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 7
gttactaccctattattgaaattttcctattcagtaacttttgtggctgtaaggatatccttttttgctgcataaattaattccccaggttgcttggaaa-----ccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
|| || | |||| || |||| ||| | | | || | || || || ||| |||| || | ||| | ||| |||||| |||||||| || ||||||||||| ||||||||||||||| |||||||||||||||| ||||| || ||||| ||||||| |||||| | ||
-----------gttctttacctttttac-tttggtaaattta--gaccaataaattactcattctta-tgtcgaaacaaatttattgaaatgaaagaaaaaaaatctagGCAACTATTGCACATGCCTTGGAGAAGACTAAATATGAAGATTCAGATATCAAGTGGAAAGAGTTTGATCCTAAATATCATTTCTCATCTCAATTTACGG
upper sequence: GLYMA18G04990.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv04s0079g00230.t01 (Vitis vinifera), 3'ss of exon 8
gttactaccctattattgaaattttcctattcagtaac---ttttgtggctgtaaggatatccttttttgctgc--ataaattaattccccaggttgcttggaaaccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
| |||| || | ||| | | || ||| ||| || | || ||| | ||| | | | ||| ||||| |||||||||| |||||||| ||||||||||||||||| |||||||| |||||||| ||||| || ||||| ||||| ||||| |||||||| ||||| | |
-----------------gtgtttttactcattagtggtagatagtttgctactaaatataaactgtcttcttgctagctacttactaatctaaaatgccctgaaactagGGAACTATTGCACATGCCTTAGAGAAGACTAAGTACGAAGATTCGGATGTCAAATGGAAGGAATTAGAGCCCAAATATCATTTCTCATGCCAATTTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taaggatatccttttttgctgcataaattaattccccaggttgcttggaaaccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
aattaat putative branch site (score: 3)
tgcataaattaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttactaccctattattgaaattttcctattcagtaacttttgtggctgtaaggatatccttttttgctgcataaattaattccccaggttgcttggaaaccagGGAACTATCGCACATGCTTTAGAGAAGACTAAGTATGAAGATTCAGATGTCAAGTGGAAAGAGTTAGATCCCAAGTATCACTTCTCATGTCAATTCATGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA