Sequence
atgc intronic sequence ATGC exonic sequencegtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
Basic information
species | Glycine max |
transcript | GLYMA11G34470.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62810.4 (Oryza sativa), 3'ss of exon 4
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgca--ttcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
|| || ||| | | ||| | | ||| | | | || | | || | || | | | | ||| ||| | ||| ||||||| |||| || || ||||||||||||||||| || |||||||| || || ||||||||||||| || | || |||||||| |||| | ||
--------------------------------------------------------------------------gtagcctacattttgcactaacactatg-gcactacatttgctgggctagggaactttgctgat-taaaactaaatgt--tttctcgaaagCTTCAGATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCC------
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g62810.3 (Oryza sativa), 3'ss of exon 2
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgca--ttcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
|| || ||| | | ||| | | ||| | | | || | | || | || | | | | ||| ||| | ||| ||||||| |||| || || ||||||||||||||||| || |||||||| || || ||||||||||||| || | || |||||||| |||| | || || ||
--------------------------------------------------------------------------gtagcctacattttgcactaacactatg-gcactacatttgctgggctagggaactttgctgat-taaaactaaatgt--tttctcgaaagcttcagATTTAGGCCAAGTATGGGGTTGGGGCTATGGAGGAGAAGGGCAACTAGGCCTGGGTTCTAGAATCCGGACTGTTTCCTCTCCACATCCTATCCCGTGCAT
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g38270.2 (Oryza sativa), 3'ss of exon 5
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
|| ||| | | ||| || | || || || || || | || || |||| | | ||| || || ||| ||| ||||||| | || ||||| |||||||||||||||||||| ||||| || || ||||| || ||||| || || | || ||||| || |||| | |||||| |
----------------------------------------------------------------gtaacttatattgggcgttta-ctgctgtatt-ctcttcacactcaactaggttaggtaagcatgctga------tcagcgaa-atattttctccaaagcttcagATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACCTTGTGT
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os05g38270.1 (Oryza sativa), 3'ss of exon 5
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
|| ||| | | ||| || | || || || || || | || || |||| | | ||| || || ||| ||| ||||||| | || ||||| |||||||||||||||||||| ||||| || || ||||| || ||||| || || | || ||||| || |||| | ||
----------------------------------------------------------------gtaacttatattgggcgttta-ctgctgtatt-ctcttcacactcaactaggttaggtaagcatgctga------tcagcgaa-atattttctccaaagCTTCAGATTTTGGTCAGGTCTGGGGTTGGGGCTATGGTGGGGAAGGACAACTAGGTTTAGGCTCTAGGATCCGGACAGTTTCCTCCCCACATCCCATACC------
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G337819_T02 (Zea mays), 3'ss of exon 5
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
||| || || | || || |||| |||| ||| | ||| | | || | || | || ||| ||||||| |||| ||||||||||||||||| ||||| || |||||||| || ||||||||||||||||| |||| || || ||||| |||| || || || ||
------------------------------------------------------------------gtaacctgcatatgtc---attatgacactgacatttgccctat--aaggatatttactgact--aaaatatttt-----------ttcctccgaaacttcagATTTAGGTCAGGTGTGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTTTGGGTTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G302245_T01 (Zea mays), 3'ss of exon 3
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaat----tttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
| | | ||| | |||| | || | | | || || | | ||| | ||| || | |||| ||||||| |||| ||||| ||||||||||| ||||| || |||||||| || ||| |||| |||||||| |||| || || ||||| |||| || || || ||
----------------------------------------------------------------------------------------gtaatctgcatttgt-cattatgacactgacattttccctgtatggatat-ttactgactaaaatatgtttcttcgaagcttcagATTTAGGTCAGGTATGGGGTTGGGGATATGGAGGAGAAGGGCAACTAGGTCTGGGCTCTAGAATCCGAACTGTTTCTTCTCCCCATCCTGTACCGTGCAT
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G55580.1 (Arabidopsis thaliana), 3'ss of exon 5
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgt-atataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctgg--aagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
|| | | ||| | | | | | | || || || || | ||||| || | | || || | || |||| || | | | ||| | | || | || || ||||||| | | | ||||||| |||||||||||||||||||| ||||| || ||||| |||||||| ||||| ||| | |||| | || ||||||||||||| |||| || ||
--------------gtgagatttttagcttttcacacaccatgtcactaatgaggtacattggttatcaattatgaaaaaaatatcagtg--gcggtatccattaagctaaagagcttttggtgtgctataataatcacttgatgcatcctaattttttttctgaagtccagATATTGGACAGGTGTGGGGTTGGGGTTATGGAGGAGAAGGACAGCTTGGATTGGGCTCTCGTGTACGTCTAGTCTCCTCTCCTCATCCTATTCCATGCAT
upper sequence: GLYMA11G34470.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0019g02280.t01 (Vitis vinifera), 3'ss of exon 5
--gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactt---tttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaat-tttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
|| | || ||| | || ||| |||| | || | ||| || || | ||| | | || | || || | | | | || ||||||| || || || | || | | | || || || | || | ||||||||||| | |||||||||||||||||||||||||| ||||| ||||| || ||||||||||| | ||||| ||||| ||||||||||||| || |||||| |
gtaaatccatgaaatcttggattgtt-gtc--cctaagcctcagttttaattcatagttctttttctgttgtggttatgcaacataggctggtactcagtatgactagaagccatggaagttctattttgtaaagcaacaaacttaatgttttctattgttcccccaagtttcagATGTTGGACAGGTGTGGGGTTGGGGCTATGGGGGTGAGGGGCAACTAGGTTTGGGTTCCCGGATACGTATGGTATCCTCTCCTCATCCTGTGCCTTGTGT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatcagttatgcattcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
cattgat putative branch site (score: 4)
attgattgtaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgactttattatgggctatttgtcaacctaggtctaaaattttatctatgctattttcgtatataatatgataatcttttggttgaagcataactttttgtgctatggaagatcagttatgcattcgaagacatgtcattgattgtaattttctggaagtttcagATATAGGACAGGTGTGGGGTTGGGGCTATGGTGGTGAAGGGCAGCTTGGTTTGGGTTCTAGAATACGAATGGTGTCCTCTCCTCATCTAGTTCCTTGTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC