Sequence
atgc intronic sequence ATGC exonic sequencegtaaagattttctattatgacaatgactaaaaccatgttctatattcaatttttaatttccatctcaaccagtgatagacacactgacttgcgtcacaatgcaacctatttgtctttcttccagAGCACTGACCAACAAGTACAAGGTGTTCTGAACCTTATTGATCTTGCTGGTAGCGAGCGGCTTTCAAAGAGTGGATCAACTGGGGACCGGTTGAAAGAAA
Basic information
species | Glycine max |
transcript | GLYMA06G41600.1 |
intron # | 13 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 13
lower sequence: AT5G54670.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaaagattttctattatgacaatgactaaaaccatgttctatattcaatttttaatttccatctcaaccagtgatagacacactgacttgcgtcacaatgcaaccta---tttgtctttcttccagAGCACTGACCAACAAGTACAAGGTGTTCTGAACCTTATTGATCTTGCTGGTAGCGAGCGGCTTTCAAAGAGTGGATCAACTGGGGACCGGTTGAAAGAAA
|| ||| | || | || | ||| | | || | || ||| || | || ||| || ||| |||||||| ||||||||||| ||||||||||||||||| ||||||| ||||||||||| || || ||||| | || |||||||||||||| || || | | |||||||
------------------------------------gtacta-accaaaccgt---ctttcttcttacagaatgtt--------tgttttgtgtgataaaccaaactggcttttttctttcttacagAGCACTGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGGAGTGAGCGTTTATCGAAGAGTGGATCAACCGGAGATAGACTTAAAGAAA
upper sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 13
lower sequence: AT4G27180.1 (Arabidopsis thaliana), 3'ss of exon 14
gtaaagattttctattatgacaatgactaaaaccatgttctatattcaatttttaatttccatctcaaccagtgatagaca--cactgacttgcgtcacaatgcaaccta--tttgtctttc--ttccagAGCACTGACCAACAAGTACAAGGTGTTCTGAACCTTATTGATCTTGCTGGTAGCGAGCGGCTTTCAAAGAGTGGATCAACTGGGGACCGGTTGAAAGAAA
|| ||| || ||| | | | | | |||| |||||| | | || | | | || ||| ||||| || |||||||| || ||||||||||||||||| ||||||| ||||||||||| ||||| ||||| | |||||||| ||||||||||| || | |||||||||
------------------------------------gtacta-atcgggtttcttactgcaacaacaacatttgatagtccgctgtttgtttctgctaaaccaacactggggtttatcttttatttacagAGCACAGAGCAACAAGTACAAGGTGTCTTGAACCTGATTGATCTTGCGGGTAGTGAGCGTTTGTCAAAGAGCGGATCAACTGGCGATAGACTGAAAGAAA
upper sequence: GLYMA06G41600.1 (Glycine max), 3'ss of exon 13
lower sequence: Vv19s0014g05070.t01 (Vitis vinifera), 3'ss of exon 13
gtaaagattttctattatgacaatgactaaaaccatgttctatattcaatttttaatttccatctcaaccagtgatagacacactgacttgcgtcacaatgcaacctatttgtctttcttccagAGCACTGACCAACAAGTACAAGGTGTTCTGAACCTTATTGATCTTGCTGGTAGCGAGCGGCTTTCAAAGAGTGGATCAACTGGGGACCGGTTGAAAGAAA
| || | | ||| | | | || || ||| | | || | | || ||| || | | || | || | || |||||||||||| |||||||||||||||||| ||||||||||||||||||| || || || || ||||| |||||||||||||| |||||||| ||||||||||
----------------gtataaagtcttcatggtgccctctgtgctgatacattgatgc---tcttgatta-tgtttta-actctgtttt----ctctttgtttttcacttatattg--accagAGCACTGAACAACAAGTACAAGGTGTTTTGAACCTTATTGATCTTGCGGGCAGTGAACGACTTTCTAAGAGTGGATCAACAGGGGACCGTTTGAAAGAAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagtgatagacacactgacttgcgtcacaatgcaacctatttgtctttcttccagAGCACTGACCAACAAGTACAAGGTGTTCTGAACCTTATTGATCTTGCTGGTAGCGAGCGGCTTTCAAAGAGTGGATCAACTGGGGACCGGTTGAAAGAAA
cactgac putative branch site (score: 2)
cctatttgtctttctt putative PPT
tatttgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagattttctattatgacaatgactaaaaccatgttctatattcaatttttaatttccatctcaaccagtgatagacacactgacttgcgtcacaatgcaacctatttgtctttcttccagAGCACTGACCAACAAGTACAAGGTGTTCTGAACCTTATTGATCTTGCTGGTAGCGAGCGGCTTTCAAAGAGTGGATCAACTGGGGACCGGTTGAAAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA