Sequence
atgc intronic sequence ATGC exonic sequencegtaggttgctgagtttgatgaaattgtctgtaattgcttcttgttgtcttttggagtaaggttttatggatttgacatgttatttttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
Basic information
species | Glycine max |
transcript | GLYMA18G46930.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os02g02290.1 (Oryza sativa), 3'ss of exon 5
--------------------gtaggttgctgagtttgatgaaat-tgtctgtaat-tgcttcttgttgtcttttgg-----agtaaggttttatggatttgacatgttatt--tttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
|| || || | | |||| ||| | | | ||| ||| || || | || | || |||||| |||| | |||| || | |||||||||||||||||||| || || || || ||||| |||||||| |||||||||||||||||||| || ||||||
gtaggccatttaccttcaacttaattttctta-tatgatataatatatatttaaaacatttcaagtctatttccaaccaccaaaaaaaatctaca-atttgatttgttgcctatccacagGTGGGCCTTCAATGGATGCTTTCCTTGTACAATAATAAGTTGAATGGTATTTTGGCTGATGAGATGGGTCTTGGCAAGACCGTACAG
upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G163849_T01 (Zea mays), 3'ss of exon 5
gtaggttg-ctgagtttga-tgaaattgtctgtaattgcttcttgttgtctt---ttggagta--aggttttatggatttgacatgttatttttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
||||| | ||| ||| | |||| | | | | | | ||| ||| | || || || | ||| ||| |||| || || |||| || | || ||||||||||| ||||| || || || || ||||| |||||||| |||||||||||||||||||| |||||||||
gtaggatatctgcttttaactgaagtaatatattcattttcaatgtagtcatggcctgtcataggagatcttaca-attcattttgttggttatgcagGTGGGCCTACAGTGGATGCTTTCTTTGTACAATAATAAGTTGAATGGCATTTTGGCTGATGAGATGGGTCTTGGCAAGACTGTACAG
upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G46020.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaggttgctgagtttgatgaaattgtctgtaattgcttcttgttgtcttttggagtaaggttttatggatt-tgacatgttatttttga--------agGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
| | | | | | ||| |||||| || | || | | | ||| |||| || | | | || | | ||||||| || ||||||||||| || |||||||| ||||||||||| || || ||||| ||||||||||||||||| |||||||| |||
-----gtatctcctccatctatactctatgttgttgcttttttctcactgtcatgccacgttttgatggtttctaaggttttttgctctgtgccaatcagGTTGGATTACAATGGATGCTATCGTTGTATAATAACAAATTAAACGGGATCTTGGCTGATGAGATGGGTCTTGGAAAAACTGTTCAG
upper sequence: GLYMA18G46930.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv15s0046g02290.t01 (Vitis vinifera), 3'ss of exon 5
gtaggttgctgagtttgatgaaattg--tctgtaattgcttcttgt----------tgtcttttggagtaaggttttatg---gatttgacatgttatttttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
||||||||| || ||| | ||||| ||| ||||| | || ||||||| ||| | || || ||| |||| | ||||||| ||||||||||||||||||||||| ||||||||| | |||||||||||||| ||||||||||||||||| ||||||||||||
gtaggttgcaatattagatacttgtcattctgtcattttgccttgtgttccactggttcctgttggagttgagttctgtgttaacaatggtatgcaatttg-gcagGTTGGGTTGCAATGGATGCTTTCCTTGTACAACAACAAACTGAATGGAATTTTGGCTGATGAGATGGGTCTTGGGAAAACTGTACAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttcttgttgtcttttggagtaaggttttatggatttgacatgttatttttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
atttgac putative branch site (score: 4)
ttattttt putative PPT
atgttatttttgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggttgctgagtttgatgaaattgtctgtaattgcttcttgttgtcttttggagtaaggttttatggatttgacatgttatttttgaagGTTGGTTTGCAATGGATGCTTTCCTTGTATAACAACAAATTAAATGGAATTTTGGCAGATGAGATGGGTCTTGGCAAAACTGTACAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG