Sequence
atgc intronic sequence ATGC exonic sequence...ttgattattacatgttgctatctagtgaagttttcgtggtcctggtcttgtatttgtctttctcagtgaaataaatacttcatgtttaacttcttttcagGGGACAAGCTGAGAAAGAATTTAAAATAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGCTGCTTGGATACTGTGTTGAGGGAGCC
Basic information
species | Glycine max |
transcript | GLYMA09G39160.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G014366_T03 (Zea mays), 3'ss of exon 1
ttgattattacatgttgctatctagtgaagttttcgtggtcctggtcttgtatttgtctttctcagtgaaataaatacttcatgtttaacttcttttcagGGGACAAGCTGAGAAAGAATTTAAAATAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGCTGCTTGGATACTGTGTTGAGGGAGCC
|||| || || | | | | | || || | || | || || |||||| | | || |||| ||||| |||||| || || ||||| || || || | ||||| |||||||||||||| || || ||||||||||| || ||| ||||||| ||||| || || || ||
cagatttttgaatactacactgttctctaggattgggttgccgtttatttcatcatgctttctgataacattatccactttttgttttctcaaacaccagGGGCCAGGCCGAGAAGGAGTTCAAGGTGGAGGTCGAAGCAATTGGTCGTGTTCGGCACAAAAATCTCGTCAGGTTGCTTGGTTACTGCGTAGAAGGTGCT
upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G01540.1 (Arabidopsis thaliana), 3'ss of exon 1
---ttgattattacatgttgctatctagtgaagttttcgtggtcctggtcttgtatttgtctttctcagtgaaataaatacttcatgtttaacttcttttcagGGGACAAGCTGAGAAAGAATTTAAAATAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGCTGCTTGGATACTGTGTTGAGGGAGCC
|| || || | || || ||| | | || | |||| || || | | | || || | || || || ||| | | || |||||| ||||| ||||| ||||| ||| |||| || |||| ||||| ||||| |||||||| |||||||||||||| | || || || || || || ||
gtttttatgggta-acgtcttta-ctaataatagcactatgcttctggattttgatctatgtga-tctgtaacatttctagttggtgtgtctttgattgccagGGGTCAAGCAGAGAAGGAATTCAAAGTAGAAGTGGAAGTCATTGGGCGAGTACGACACAAGAATCTTGTTAGGCTTTTAGGGTATTGCGTGGAAGGTGCA
upper sequence: GLYMA09G39160.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv15s0046g02030.t01 (Vitis vinifera), 3'ss of exon 1
ttgattattacatgttgctatctagtgaagttttcgtggtcctggtcttgtatttgtctttctcagtgaaataaatacttcatgt--ttaacttcttttcagGGGACAAGCTGAGAAAGAATTTAAAATAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGCTGCTTGGATACTGTGTTGAGGGAGCC
| || | | | |||| | | | | | | | || | | | | || | | ||| | ||| |||| || ||| || ||||||||||| ||||| ||| | ||||| ||||| || || || || || ||||| |||||||||||| |||| |||||||||| |||||||||
-tctttctcaatagctgctcaacaataatttgcatattatttccatttttcttatatttagatcttttgtgcat-taccttatgagattaatgaattaccagAGGCCAAGCTGAGAAGGAATTCAAAGTGGAGGTTGAAGCCATAGGCCGGGTCCGGCACAAGAATCTTGTTAGGTTGCTGGGATACTGTGCTGAGGGAGCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgtatttgtctttctcagtgaaataaatacttcatgtttaacttcttttcagGGGACAAGCTGAGAAAGAATTTAAAATAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGCTGCTTGGATACTGTGTTGAGGGAGCC
gtttaac putative branch site (score: 3)
tttaacttcttttc CT-rich tract
aaataaatacttcatg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttgattattacatgttgctatctagtgaagttttcgtggtcctggtcttgtatttgtctttctcagtgaaataaatacttcatgtttaacttcttttcagGGGACAAGCTGAGAAAGAATTTAAAATAGAGGTAGAAGCAATTGGTCGAGTGCGACACAAAAATCTTGTTAGGCTGCTTGGATACTGTGTTGAGGGAGCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - tgttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtt