Sequence
atgc intronic sequence ATGC exonic sequence...gagcattaggtttatgattttgtgattcgcgattaattaatctttatacactgctgccttagttatattgtttgactttgaggggattattctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
Basic information
species | Glycine max |
transcript | GLYMA09G40480.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os03g14260.2 (Oryza sativa), 3'ss of exon 7
--gagcattaggtttatgattttgtgattcgcgattaattaatctttatacactgctgccttagttatattgtttgactttgaggggattat---------tctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
|| | || || || || |||| || || ||| | || || || ||||| | | | | |||| | ||| | |||||||| |||||||| |||||||||||||| ||||||||||| |||||||| | |||||||| ||||| || |||||||| || | || || ||||||
gtaagtacagggcttcctatattcagatt-gcaatgtatttccccatacttttctttgatgtatttatagtatataggcagtatatgattgtgtttccctttctcttgtagGCACTACAATATGAATCGCATCAGGCTTGTCTGGTCAAGCATATGGCATGTCTTGTCTGATTTTTTTGTTACAATTGGCTGCTCAGAGAATCTCTCAATT
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G058870_T01 (Zea mays), 3'ss of exon 7
-----gagcattaggtttatgattttgtgattcgcgattaattaatctttatacactgctg-----ccttagttatattgtttgactttgaggggatt-attctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
|| | ||| || | | | | | | ||| | ||| |||| | ||| |||| | | || ||| ||| || || | ||||| || ||||||||||||||||| ||||| |||||||| || |||||||| | |||||||| ||||| ||||||||||| || | ||| ||||||||
gtaaggaatctgaggctt-tattatcattactacattgcaatgtgtttttttacatttctgttcggtcttatagacagtgcatgattttttttttttttgccctcttgtagGCATTACAATATGAACCGCATCAGACTTGTTTGGTCAAGTATATGGCATGTCTTGTCTGATTTTTTTGTCACCATTGGCTGCTCAGAAAATCTTTCAATC
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: AT3G60860.1 (Arabidopsis thaliana), 3'ss of exon 7
---------------gagcattaggtt-tatgattttgtgattcgcgattaattaa---tctttatacactgctgccttagttatattgtttgactttgaggggattat--tctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
| || | | | | | | || ||| | ||| | | | || | ||| ||| | || |||| | | || | | ||| ||||||| ||||| ||||| ||||| |||||||| ||||||||||| ||||| || || || | ||||||||| |||||||| || || | || ||||| |||
gtaagaatctcctagtttcgttcctctctgttctctcatatactgcatataagagacgttctctgttcttagcaactttaagtatgtagtctgacaattttctgtttgtcatttgtgacagGCATTATAACATGAATCGCATAAGGCTTGTTTGGTCAAGCATCTGGCAAGTGCTATCAGGTTTCTTTGTGACCATTGGATGCTCAGAGAATCTTTCTATT
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G01960.1 (Arabidopsis thaliana), 3'ss of exon 7
gagcattaggtttatgattttgtgattcgcgattaattaatctttatacactgctgccttagttatattgtttgactttgaggggattattctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
| ||| | | |||| | | || | ||| |||| || |||| ||||| | |||| | || |||||||||||| ||||||||||| || ||||| ||||| ||||| |||||||| ||||||||||||||||| || ||||||||||||| ||||| || |||
----gtaaggatcaatcttttctttacgatatctgttttgtttttgctcact-ctctcttatttataccct----gtttgttgtaat--------ggcagGCACTATAACATGAACCGCATAAGACTTGTCTGGTCGAGCATCTGGCATGTGCTCTCTGATTTCTTTGTGACTATTGGCTGTTCTGATAACCTCTCCATT
upper sequence: GLYMA09G40480.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv15s0048g00800.t01 (Vitis vinifera), 3'ss of exon 7
-----------------------------gagcattaggtttatgattttgtgattcgcgattaattaatctttatacactgctgccttagttatattgtttgactttgaggggatt-attctgta----acagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
| |||| | || ||| ||| | ||| || ||| | ||||| ||| || ||| | | || | | |||| || | | ||||||||||||| |||||||| ||||||||||| ||||||||||| |||||||| ||||| |||||||||||||||||||||||||| | ||||||||||||
gtatgaatcattctcaatttgtcttgttcatgttttagcataccatattagtgcttcatttattatttatatttgtcagctgcta--ttaaaaattttgctaaaattctaagtgatttgttttcttttacacagGCACTATAACATGAACCGTATCAGGCTTGTGTGGTCAAGCATCTGGCATGTACTCTCAGATTTCTTTGTAACCATTGGCTGTTCAGAGAACCTTTCAATT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacactgctgccttagttatattgtttgactttgaggggattattctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
gtttgac putative branch site (score: 4)
ttattct putative PPT
ttagttatattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gagcattaggtttatgattttgtgattcgcgattaattaatctttatacactgctgccttagttatattgtttgactttgaggggattattctgtaacagGCACTATAATATGAACCGCATCAGGCTTGTATGGTCAAGCATTTGGCATGTTCTCTCTGATTTCTTTGTAACCATTGGCTGTTCTGGAAACCTTTCAATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - -ttttgtg
- - - - - - - - - - - - - - - - - - - - - - - - cactgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgtttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgagggg