Sequence
atgc intronic sequence ATGC exonic sequence...gtgctttttatcaagttagatcagtttgctttatttcaattatggtgtcatgtcattcccggtaatgtgctctctaaatcaagtttctccatttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT
Basic information
species | Glycine max |
transcript | GLYMA10G11100.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G010353_T02 (Zea mays), 3'ss of exon 2
gtgctttttatcaagttagatcagtttgctttatttcaattatggtgtcatgtcattcccggta---atgtgctctctaa-atcaagtttctccatt-tatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT
|| |||| || | | || || ||| | |||| | ||| | ||| | || | | | | ||| || ||| ||| | | |||| ||||| ||||| ||||||||| | ||||||| |||| | ||||||||||||||| ||| | ||||| || |||||||| ||||| || || |
----gttagatcaggtcaactttgtatgtgctatct-aattgtcagcacatatacttcttgttacttttattgtatataatatgaaggctctttttcgtccccagATTGGATCAACTGAATGGGTTGAAGACAACCTTGAAGATCTGCATTCCAAAGCTGTAGCTTACTTGAATGTTGATTGTGCTGTGCAAGGTGTGGGATTTT
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0285g00060.t01 (Vitis vinifera), 3'ss of exon 2
----gtgcttt-----ttatcaagttagatcagtttgctttatttcaattatggtgtcatgtcattcccggtaatgtgctctctaaatcaagtttctccatttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT
|| | | | ||| | |||| | | ||| | ||||| ||| | |||| || | | | | | | | | | || || || ||||||||| ||||||||||| |||||||||||| | ||||| |||| |||| |||||||||||| |||||||||||||| |||||||| || || ||||
ttatttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgt-atttaacactcaaaagtaatttacttgtgttgtgtggcttca--------gATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0319g00060.t01 (Vitis vinifera), 3'ss of exon 1
--gtgcttt-----ttatcaagttagatcagtttgctttatttcaattatggtgt-catgtcattcccggtaatgtgctctctaaatcaagtttctccatttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT
|| | | | ||| | |||| | | ||| | ||||| ||| | |||| || | | | | | | | | | || | || ||||||||| ||||||||||| |||||||||||| | ||||| |||| ||| |||||||||||| |||||||||||||| |||||||| || || ||||
atttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatttaacactcaaaagtaatttacttgtgttgtgtggcctca--------gATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTGAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv08s0032g00670.t01 (Vitis vinifera), 3'ss of exon 2
---gtgcttt-----ttatcaagttagatcagtttgctttatttcaattatggtgt-catgtcattcccggtaatgtgctctctaaatcaagtttctccatttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT
|| | | | ||| | |||| | | ||| | ||||| ||| | |||| || | | | | || || | | | | ||| | ||| |||||||||| ||||||||||| |||||||||||| | ||||| |||| |||| |||||||||||| |||||||||||||| |||||||| || || ||||
tatttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatttaacactc---aaagtaattt---acttgtgttgcgtggttt---cagATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0352g00020.t01 (Vitis vinifera), 3'ss of exon 2
--gtgcttt-----ttatcaagttagatcagtttgctttatttcaattatggtgt-catgtcattcccggtaatgtgctctctaaatcaagtttctccatttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT
|| | | | ||| | |||| | | ||| | ||||| ||| | |||| || | | | | | | | | | || | || ||||||||| ||||||||||| |||||||||||| | ||||| |||| |||| |||||||||||| |||||||||||||| |||||||| || || ||||
atttgttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatttaacactcaaaagtaatttacttgtgttgtgtggcctca--------gATAGGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCT
upper sequence: GLYMA10G11100.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv00s0327g00020.t01 (Vitis vinifera), 3'ss of exon 1
---gtgctttttatcaagttagatcagtttgctttatttcaattatggtgt-catgtcattcccggtaatgtgctctctaaatcaagtttctccatttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT--
| | ||| | |||| | | ||| | ||||| ||| | |||| || | | | | | | | | | || | || || | ||||| ||||||||||| |||||||||||| | ||||| |||| |||| |||||||||||| |||||||||||||| |||||||| || || ||||
gttctaaaagtaatccaattagctaggcttgttctatttgaatggttgtgtgtatttaacactcaaaagtaatttacttgtgttgtgtggcctcagatagG------GGATCTACTGAGTGGGTCGAACAAAACCTTTTGAATCTGGGTTCTAAAGTTGTAGCATACCTTAATGTAGACTGTGCAGTTCAAGGACCAGGCTTCTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtcatgtcattcccggtaatgtgctctctaaatcaagtttctccatttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT
ctctaaa putative branch site (score: 3)
tttctccattt putative PPT
atttatgta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgctttttatcaagttagatcagtttgctttatttcaattatggtgtcatgtcattcccggtaatgtgctctctaaatcaagtttctccatttatgtagATAGGATCCACTGAGTGGGTTGAACAAAACCTTGTCAATCTTCGTTCCAAAGCTGTAGCATACCTCAATGTAGACTGTGCTGTTCAAGGGCCTGGTTTCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
-tgctttt
- - - - - - - - - - - - - tgcttta
- - - - - - - - - - - - - - - - - - - - - tggtgtc
- - - - - - - - - - - - - - - - - - - - - - - - - - -cattccc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaatcaag