Sequence
atgc intronic sequence ATGC exonic sequencegtaagtgactttgttgcactcttgcatggtaacattcagttatgatatcctacattctttctaaatcctaatgaatgaatgactttcacttctgaaattgttatgtaaacagTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
Basic information
species | Glycine max |
transcript | GLYMA14G39070.1 |
intron # | 11 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os02g58480.1 (Oryza sativa), 3'ss of exon 8
gtaagtgactttgttgcactcttgcatggtaacattcagt-tatgatatcctacattctttctaaatcctaatgaatgaatgactttcacttctgaaattgttatgtaaacagTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
| | || | | | || |||| | ||| | || || | || | | || || ||| || | | | || || ||| || | ||||| || ||||| |||||||||||||| ||||||||||| ||||| | |||||| | || ||| | || ||||||||||| |||||
---------gtaagtacatcccttgggaagcatatccagtatgcaggatcttttttttttacagcat--tgctttattaacaactcgcatcacatgtggtatgattaaatcagAGGGCACCTAGCAGACAGGAGTAAGCCAATCATCTTTTCAATGGCAAGACTTGACAAGATAAAGAACATCACAGGGCTGGTCGAATGGTATGGTCAGAAC
upper sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g17650.1 (Oryza sativa), 3'ss of exon 11
-------------------------------gtaagtg-actttgttgca---------ctcttgcatggtaacattcagttatgatatcctacattcttt--ctaaatcctaatgaatgaatgactttcacttctgaaattgttatgtaaac-agTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
| || | || | | | || ||||| | || | || | | || | | || || || ||| | ||||| || ||||| | | || | || ||||| || || ||||| || || |||| || |||||||||||||| ||||||||||||||| || || ||| |||| ||| | || || ||||||||| |||||
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttctcttttactgttagatcagatca-gacaacttaagttggttaattaagtgctaattgctgc----tcttcaccttt----ttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
upper sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 11
lower sequence: LOC_Os04g24430.1 (Oryza sativa), 3'ss of exon 11
-------------------------------gtaagtg-actttgttgcactcttgcatggtaacattcagttatgatatcctacattctttctaaatcctaatgaatgaatgactttcacttctgaaattgtt---atgtaaac-agTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
| || | || | | | || | | | | | | |||| | | | || ||||| || | | | || | | || || || ||||| || || ||||| || || |||| || |||||||||||||| ||||||||||||||| || || ||| |||| ||| | || || ||||||||| |||||
gtaagctactacccggacggccaggctccttggaaacgtacctagctacaaattaacttc-tcttttactgttagatcagatcagacaacttaagttggctaattaagtgctaattgctgctcttcacctttttttaatttaaaccagAGGGTATCTGGCAGACAGGAACAAACCAATCATCTTCTCGATGGCAAGGCTTGATAAGGTAAAAAACATAACTGGGCTTGTGGAGTGGTATGGCCAGAAC
upper sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 11
lower sequence: AT5G37180.1 (Arabidopsis thaliana), 3'ss of exon 9
----------------------------------------------gtaagtgactttgttgcactcttgcatggta--acattcagttatgatatcctacat-------tctttctaaatccta---atg---aatgaatgactttcacttctgaaattgttatgta-aacagTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
||| | || | | | | || | || | | | | | | |||| | | | || ||| || ||| | | || | | || | || || || | || || || ||| ||| || | || ||| || ||||| |||||||||||||||||||||||||| || ||| ||||||| ||| ||| ||||||| |||||||
gtacgtctctattccctattttacttttccacaatactacacggtctcaagaagcgttatag-attgttatagaatatgaaactaactattaatattatttgtaagtaaatgttatagaatgttatctatgtgtattaaaaaatactaaccgatatttttcttgtgaacaaaagCGGTTATTTAGTGGACAAGAAGAAACCGATCATTTTCTCAATGGCAAGGCTTGATGTTGTCAAAAACCTAACCGGATTAACTGAGTGGTATGCCAAGAAC
upper sequence: GLYMA14G39070.1 (Glycine max), 3'ss of exon 11
lower sequence: Vv04s0079g00230.t01 (Vitis vinifera), 3'ss of exon 10
gtaagtgactttgttgcactcttgcatggtaacattcagttatgatatcctacattctttctaaatcctaatgaatgaatgactttcacttctgaaattgttatgtaaacagTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
||| || | | || | | | ||| | |||| | ||| | | | | | | ||| ||||| ||| || | | ||||||||||| |||||| || || | ||| || ||||||||||||||||||||||| || | ||||||||| | || |||||| ||| |||| || || |||
gtaggttttgaaagggaaatcatttgttcaattatttatttataactacct---tgcagtttggaattttatgtctgaattactaacatctggtctgaaccttgaaaaacagTGGATTTCTAGCAGACAGAAAGAAACCTATCATCTTCTCAATGGCAAGGCTGGACATAGTGAAGAACATTACGGGGTTAACTGAGTGGTTCGGGAACAAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttctaaatcctaatgaatgaatgactttcacttctgaaattgttatgtaaacagTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
tcctaat putative branch site (score: 2)
aaattgttatgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtgactttgttgcactcttgcatggtaacattcagttatgatatcctacattctttctaaatcctaatgaatgaatgactttcacttctgaaattgttatgtaaacagTGGATATCTAGCTGATAGGAGGAAGCCAATCATCTTCTCAATGGCAAGGCTTGATGTTGTGAAGAACTTAACCGGGTTAGTTGAATGGTATGGCAAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC