Sequence
atgc intronic sequence ATGC exonic sequencegtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
Basic information
species | Glycine max |
transcript | GLYMA07G40300.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 9
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
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--------------gtaaattcaaaagcccttctag----aattaattttagagtgggcacactttgcttatgatgattactgttatctttatattct----------agATTGTCCTGGAAGCCGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGTTTAAAATCCTTAATAAAAGGAGTACTTGAAATGGCAAAGGAGCCAT
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 9
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
| ||| | | | | | | || | ||| || | || | || | ||||| | || | ||| |||||||| | ||||| ||||| |||||||| || || || |||||||||||||| ||||| ||||| || || || | || |||||||||||||||
-------------gtaagattggatccagtttcaggattagtgctactatcaggcattttcccatcttttatgaacactgaa-cagtattctc----tgac--attctagATTGTCTTGGAAGCCGATGGTTATCAACCGTACCTGATATCTCCAGAGAAAGGGTTGAGGTCCTTGATAAAGATAGTATTGGATATGGCAAAGGAGCCAT
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 9
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctc-ttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
||| | | | | ||||| | |||| ||| ||| || || | | || || | | | | | | | |||||||| | ||||||||||| |||||||| ||| | || |||||||||||||| |||||||||||||| ||| || || ||| |||||||||||||||
-------------------------gtat-gatcacttccaattt--tacattgagctctggttggcagtta--gcacatgattaaacacatttctctccacacaat--agATTGTCTTGGAAGCAGATGGTTATCAACCATATTTGATATCTCCAGAGAAAGGGTTGAGATCCTTAATAAAAATAGTACTGGAAATGGCAAAGGAGCCAT
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattt-tattctcttgacacttgag-gtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
|| ||| | | || | | |||| | | || ||| | ||| ||| ||| | || || |||| ||| |||||||| || | || || ||||| |||||||||||||| || |||||||||||||| |||||||| ||||| ||| ||||||||| |||| || || |||
--------------gtgggtttctgaattttcctgcctcaaattgtataaacaagtaacggctttagactggagtgtgacagattg-attttccaatt-------gtttcagATCGTGTTGGAGGCTGATGGTTATCAACCTTATCTCATATCTCCAGAGAAAGGGTTGAGATCGTTAATAAAAACCGTTCTTGAGTTGGCTAAAGACCCAG
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 9
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
|| | | | | ||| || || | | | | |||| |||||| ||| |||| |||| | ||||| |||| | || |||||||| ||||||||||||||||| |||||||||||||| |||||||| || || || || ||||| |||| || || ||
--------------gtgggtgtcttcttctgtcc---taagtttctgcacgagacaag-ttttgagacttga----tttgtcaaaatatc-----tttgatt---ttcagGTTGTTTTGGAGGCAGATGGTTATCAACCTTATCTTATATCTCCAGAGAAAGGGTTGAGATCGTTGATAAAGATTGTCCTTGAGTTGGCTAAAGACCCGG
upper sequence: GLYMA07G40300.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 9
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
||| ||||| || ||| | || || |||| | | | || | | | | | || |||| || |||| ||| | || |||||||| || ||||||||||| ||||||||||||||||| |||||||| |||||||| || || |||| ||| || || || ||||| || |||||||
gtatgg-ttctctttt--attcacattccaacttttgtgcctttta----aatatgttgttgtaaggcctttattgtttgc---aatgttcct-tttcaattgataccagATTGTGCTAGAAGCAGATGGTTATCAACCTTATCTTATATCTCCAGAAAAAGGTTTAAGGTCTCTAATAAAAATTGTCCTGGAGCTGGCGAAAGAGCCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
tcttgac putative branch site (score: 3)
cttatttc putative PPT
ttctatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaaccttctcccttgaatttgtcatattgtttaggtagaatttagttcattttattctcttgacacttgaggtgcttgcttctatattcccattttggcttatttcagATTGTCCTTGAAGCAGATGGATATCAACCTTATCTTATCTCTCCAGAGAAAGGTTTGAGATCCTTAATTAAAGGCGTTCTTGAACTGGCAAAGGAGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG