Sequence
atgc intronic sequence ATGC exonic sequencegtatactaagcaagaatttaaccttgtcctgccgaaaccttttcaaattttaagttggttttactaatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTGTTAGATATTACTGACTTTTCTGTGAAG
Basic information
species | Glycine max |
transcript | GLYMA16G29040.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g12660.1 (Oryza sativa), 3'ss of exon 2
-------gtatactaagcaagaatttaaccttgtcctgccgaaaccttttcaaattttaagttggttttactaatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTGTTAGATATTACTGACTTTTCTGTGAAG
||| | | | | |||| | ||| ||| | | | | | || | ||| ||| ||| | ||| ||||||||| |||||||||||||||||||||||| | || || || |||||| |||| ||||||||| ||||| ||| || ||| | |||
gtaaatcatattccattgcacaggttaag---gagttgctgaatcactcttct-tctggccctgactaagttaaggctaattaagttcctatcttgaagAACTTTACCAGCAAATGCTTGCCAAAGCGCTTGCCCACTATTTTGAAGCAAAATTGCTGTTGCTAGATCCTACAGATTTTCTCATAAAG
upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01850.t01 (Vitis vinifera), 3'ss of exon 3
------------------gtatactaagcaagaatttaacc--ttgtcctgccgaaaccttttcaaattttaagttggtt-----ttact--aatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTGTTAGATATTACTGACTTTTCTGTGAAG
|| || | | | |||| || | | | || |||||| | ||| ||| || || || | | ||||| | || ||||||||||| ||||||||||| |||||||||||||||||||||| ||||||| ||||||||||| | || ||| ||| |||||||||| | |||
gtatgctctctggaatatgttctctgaccctgcatttggatatttatgtttctgagtccttttgatggcctaacttgtttgccttttgctttacttttatttttgttaatcttttgaagAACTTTACCAGCAAACACTTGCCAAAGCTTTAGCACATTTCTTTGAAGCAAAGTTGCTGCTATTGGATGTTAATGACTTTTCTCTAAAG
upper sequence: GLYMA16G29040.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0050g01840.t01 (Vitis vinifera), 3'ss of exon 3
------------gtatac-taagcaagaatttaaccttgtcctgccgaaaccttttcaa-attttaagttggtt-----ttact--aatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTGTTAGATATTACTGACTTTTCTGTGAAG
| ||| | | | || | || | | | | |||||| | || |||||| || || | | |||| | ||| || |||||||| ||| |||| | || ||||||||||||||||| | ||||||| ||||||||||| |||| ||| ||| |||||||||| | |||
gtatgttgtctggaatatgtgatctgatatggatatttatgtttcttagtccttttaattggcccaatttggttgccttttgcttcatttttattcttgtttatcttctgaagAACTTTATCAGCGAGCACTCGCCAAAGCTTTAGCACAATTCTTTGAAGCAAAGTTGCTGCTGTTGGATGTTAATGACTTTTCTCTAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttttcaaattttaagttggttttactaatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTGTTAGATATTACTGACTTTTCTGTGAAG
tactaat putative branch site (score: 1)
ttttactaatactatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatactaagcaagaatttaaccttgtcctgccgaaaccttttcaaattttaagttggttttactaatactatttacttatatattttgaagAACCTTACCAGCAAATGCTTGCCAAAGCTTTAGCACATTACTTTGAATCAAAGTTGCTGTTGTTAGATATTACTGACTTTTCTGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT