Sequence
atgc intronic sequence ATGC exonic sequencegtagatgttaagttactatattgtttatttgtcattggaaatgtgcaaagatatttgattcattgtaactactagtcttttttctttctcttttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
Basic information
species | Glycine max |
transcript | GLYMA06G18810.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os02g38010.1 (Oryza sativa), 3'ss of exon 5
-gtagatgttaagttactatattgtttatttgtcattggaaatgtgcaaagatatttgattca-ttgtaactactagtcttttttctt-tctctttt-aacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
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gttaactggttatcttctgtttcttgtttcaattgttgagcacttgagctactattagataaaactgactcaaaaaatctcacctgttatttctattgaacagTGGAACTTCCGTATTGGCTTTACTCCCAAAGAAGGTTTAGTTATTCATTCTGTTGCATATGTTGATGGAAACCGTGGGCGTCGACCTATCGCTCACAGGC
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g40040.1 (Oryza sativa), 3'ss of exon 6
gtagat-gttaagttactatattgtttatttgtcattggaaatgtgcaaagatatttgattcattgtaactactagtcttttttctttctcttttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
|| || ||| || | | || | |||| | || || | ||| |||||| | || || || || |||| | || | |||||||| ||||||||||| ||||| || ||||| |||||||| || ||||||||||||||||||||||| || | |||||| |||| | ||||||||||
gtgcattgttgtgtaaagcttttctctatt-atgatgagataaacaaaaaaatattt--ccccctggaattaataacacttttaatgatg--ttgagcagTGGAACTTCCGTATTGGCTTCACCCCTAAAGAGGGTTTGGTCATCTATTCTGTTGCATATGTTGATGGCAGCCGTGGACGTCGGCCGATAGCTCATAGGC
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os04g04950.1 (Oryza sativa), 3'ss of exon 5
-gtagatgttaagttactatattgtttatttgtcattggaaat--gtgcaaagatatttgattcattgtaactactagtcttttttctttctcttttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
|| || | || | || | ||| || || | | | ||| | || | | | || | |||||| | | |||||||||| || |||||||| ||||| || ||||||||||| ||| | |||||||||||||||||||||| | | ||| || | ||| | ||||| ||||
gttaactggctatctatagtgtttactgttttaatttaattattggcgtagtagtatctaataaaa-atgattaaaaaaacattttctgt-----tgaacagTGGAACTTTCGTATTGGCTTCACCCCTAAAGAAGGTTTAGTTCTTCATTCTGTTGCATATGTTGATGGAAACCGTGGCCGTCGACCTATCGCTCACAGGC
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G147884_T01 (Zea mays), 3'ss of exon 5
gtagatgttaagttactatattgtttatttgtcattggaaatgtgcaaagatatttgattcattgtaactactagtcttttttctttctcttttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
|| | | | ||||| | || || || | | | || ||| | ||| || || | || || | || | |||||||| ||||||||||| ||||| |||||||| ||||||||||| ||||||||||| |||||||||||||| | |||||| || ||| | || |||||||
-----------gtaattgt-ttgttgaactg-cagtgctagtatt--aacataatgtcttc--tgaaataaataacacttaatggttat-----ggcagTGGAACTTCCGTATTGGCTTCACCCCCAAAGAGGGTTTGGTTATCTATTCTGTTGCTTATGTTGATGGTAGCCGTGGACGTAGACCTATAGCACATAGGC
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv17s0000g09100.t01 (Vitis vinifera), 3'ss of exon 5
gtagatgttaagttactatattgtttatttgtcattggaaatgtgcaaagatatttgattcattgtaactactagtcttttttctttctctt--ttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
| || ||| || | | | |||| | | | | |||| | ||| ||| ||| |||| | ||| | | || || |||||||||||||||||||| ||||| |||| ||| ||||||||||| ||||||||||||||||||||||||||| || ||||| ||||| |||||||||
--gtacttttggtttcttga--gctggcttgttaataaatgtaattaaagtcaga-gatgcatactaaacactatcaatgttttatctttttggttggcagTGGAATTTCCGTATTGGTTTCACTCCCAGAGAGGGTTTGGTTATCCATTCTGTTGCATATGTTGATGGTAGTCGGGGTCGAAGACCTGTAGCTCATAGGT
upper sequence: GLYMA06G18810.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S9_129V6.1 (Physcomitrella patens), 3'ss of exon 6
-------------------------------------------------------------------------------gtagatgttaagttactatattgtttatttgtcattggaaa----tgtgc---aaagatatttgattcattg--taactactagtcttttttctttctcttttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
|| || | | | | || | || | | | ||||| ||| | | | | | |||||| | || | ||| | ||||||||||| || || ||||||||||| ||||||||||||||||| | | ||||| |||| |||||||||| ||| || | | |||| ||| |
gtaccaaattggagaatgttttggacccgatttcattatgacgagagcttaatgtgcttgaactcatgaatgattctcaataattggaacacgattctgttctctaccagcagtgaggtgcttttgtgcgacaaatgaactcctctgttcgactaactattcatcgtgttttgaaacacctatgcagTGGAATTTTCGGATCGGATTCACACCAAAAGAAGGTTTGGTTATTCACACGGTTGCTTATGAAGATGGTAGTCGAGGAAGACGATCAATTGCACATCGTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcaaagatatttgattcattgtaactactagtcttttttctttctcttttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
ttgtaac putative branch site (score: 2)
ctactagtcttttttc CT-rich tract
atatttgattcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtagatgttaagttactatattgtttatttgtcattggaaatgtgcaaagatatttgattcattgtaactactagtcttttttctttctcttttaacagTGGAATTTCCGTATTGGATTCACACCCAAAGAAGGTTTGGTTATATATTCTGTTGCATATGTTGATGGTAGTCATGGACGAAGGCCTGTTGCTCATAGGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA