Sequence
atgc intronic sequence ATGC exonic sequence...atttgattatttcatgttgctatctagtgaagttttcccggtcctggtcttgtatttgtcttcctcagaaataaatacctcatgtttaacttattttcagGGGACAAGCTGAGAAAGAATTTAAAGTAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGTTGCTTGGATACTGTGTCGAGGGAGCC
Basic information
species | Glycine max |
transcript | GLYMA18G47170.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
---atttgattatttcatgttgctatctagtgaagttttcccggtcctggtcttgtatttgtcttcctcagaaataaatacctcatgtttaacttattttcagGGGACAAGCTGAGAAAGAATTTAAAGTAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGTTGCTTGGATACTGTGTCGAGGGAGCC
|||| || | || | ||||| | || ||| | | | | || | | | || || | ||||| | |||||| || || ||||| || || || || ||||| |||||||||||||| || || ||||||||||| || ||||||||||| ||||| || || || ||
cagatttttgaatactacactgttctctaggattgggttgccgtttatttcatcatgctt---tctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT
upper sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 1
atttgattatttcatgttgctatctagtgaagttttcccggtcctggtcttgtatttgtcttcctcagaa-ataaatacctcatgtttaacttattttcagGGGACAAGCTGAGAAAGAATTTAAAGTAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGTTGCTTGGATACTGTGTCGAGGGAGCC
||| | | | || || ||| | | | | |||| || || | | | || || || | ||| | | ||| |||||| ||||| ||||| ||||| |||||||| || |||| ||||| ||||| |||||||| |||||||||||| | | || || || || || || ||
gtttttatgggtaacgtcttta-ctaataatagcactatgcttctggattttgatctatgtgatctgtaacatttctagttggtgtgtctttgattgccagGGGTCAAGCAGAGAAGGAATTCAAAGTAGAAGTGGAAGTCATTGGGCGAGTACGACACAAGAATCTTGTTAGGCTTTTAGGGTATTGCGTGGAAGGTGCA
upper sequence: GLYMA18G47170.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 1
----atttgattatttcatgttgctatctagtgaagttttcccggtcctggtcttgtatttgtcttcctcagaaataaatacctcatgt--ttaacttattttcagGGGACAAGCTGAGAAAGAATTTAAAGTAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGTTGCTTGGATACTGTGTCGAGGGAGCC
| || | | || | | | | || || | | ||| ||||| | | || ||||| ||| |||| ||| ||| || ||||||||||| ||||| ||||| ||||| ||||| || || || || || ||||| ||||||||||||||||| |||||||||| ||||||||
tctttctcaatagctgctcaacaataatttgcatattatttccattttt---cttatatttagatcttttgtgcat---taccttatgagattaatgaattaccagAGGCCAAGCTGAGAAGGAATTCAAAGTGGAGGTTGAAGCCATAGGCCGGGTCCGGCACAAGAATCTTGTTAGGTTGCTGGGATACTGTGCTGAGGGAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtcttgtatttgtcttcctcagaaataaatacctcatgtttaacttattttcagGGGACAAGCTGAGAAAGAATTTAAAGTAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGTTGCTTGGATACTGTGTCGAGGGAGCC
gtttaac putative branch site (score: 3)
cttattttc CT-rich tract
atgtttaacttatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atttgattatttcatgttgctatctagtgaagttttcccggtcctggtcttgtatttgtcttcctcagaaataaatacctcatgtttaacttattttcagGGGACAAGCTGAGAAAGAATTTAAAGTAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGTTGCTTGGATACTGTGTCGAGGGAGCC
- - - - - -tcatgtt
- - - - - - - tgttgct
- - - - - - - - - - - - - - - - - - -ccggtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa