Sequence
atgc intronic sequence ATGC exonic sequence...agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttcaaattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
Basic information
species | Glycine max |
transcript | GLYMA09G17040.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv08s0007g06520.t01 (Vitis vinifera), 3'ss of exon 1
agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttca--aattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
|| ||| | | ||| | | || |||| | | | | ||||| || | || || ||| ||| | | | || ||||||||||||||||||||||||||||| ||||| ||||| ||||||||||||||| | || || |||||||| ||||||||||| ||||| || || ||||
-gtattgattcagaatccaaaatgttgtttgagtttgtgggattgattggatttggagaa-tacccagttgcttatttctttgattctttctgaaatttcagGCTGGATTTGCTGGAGATGATGCTCCGAGGGCTGTGTTTCCTAGCATTGTGGGTAGACCTCGACACACTGGAGTGATGGTTGGGATGGGACAGAAAGATG
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
lower sequence: EDO98923 (Chlamydomonas reinhardtii), 3'ss of exon 1
-agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtact-tcaaattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
||| ||| | || | | | | | | | | | || | || | || | || | | | | ||||||||| |||||||| |||||||| || | || |||||||| ||| ||||| || || |||||||| ||||||||||| || ||||| || |||
tccatttaacttgggcgttgggcctggcgtgggccccgcgctgcag--cgcgttgttcgagcaaacctgatgctggcgatcgctgtgtcgccgtgtccgcagGCTGGCTTTGCTGGTGATGATGCCCCTCGCGCTGTGTTCCCCTCCATCGTGGGCCGGCCCCGCCACACCGGTGTGATGGTCGGGATGGGCCAGAAG----
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S198_154V6.3 (Physcomitrella patens), 3'ss of exon 2
agttttgtcttttggtttttga--tgatactagattttgacccgt--gggatacaaagagagaactaattgggtgagtacttcaaattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
| || ||| | | | | || | || | | || || | || | ||| | |||||| | || || |||||||||| || ||||||||||| || || | |||||||| || ||||| ||||| || || | ||||||||||||||||| || ||||| || ||||| |
aaccttaacttgcgtaccctcaatttttatcatcacttcatctgtctggagttcacatctcttg-taacatgatgagtaatcacgtgcggatt---ttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S198_157V6.3 (Physcomitrella patens), 3'ss of exon 2
-----------------------------------------------------------------------------------agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttcaaattatgttcaattt-tgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
|| || | | | | || | || ||||| || | | | | || ||| || | ||| |||||||||| || ||||||||||| || || | |||||||| || ||||| ||||| || || | ||||||||||||||||| || ||||| || ||||| |
gtatgatattaactgttttgatgatgcatttgtattctccctatgtgatgaagtggcttgcaataaaatgcagttctaaagcatgtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S198_157V6.1 (Physcomitrella patens), 3'ss of exon 2
agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttcaaattatgttcaattt-tgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
|| || | | | | || | || ||||| || | | | | || ||| || | ||| |||||||||| || ||||||||||| || || | |||||||| || ||||| ||||| || || | ||||||||||||||||| || ||||| || ||||| |
-gtcatgggccaagctgggtcgttatcgtcttcttcacatcgtggtatctctgtgatcggcacaaaacctaaaatgttggtattgtgcggattttatgcagGCTGGTTTCGCTGGAGATGACGCCCCCCGCGCCGTGTTTCCGAGCATCGTGGGACGGCCGAGGCACACTGGTGTGATGGTCGGTATGGGACAGAAGGACG
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ17401 (Selaginella moellendorffii), 3'ss of exon 1
agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttcaaattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
||| | | | | | | | | || | | | ||| | ||||||||||||||||| ||||| |||||||| ||||||||||| || ||||||||||| || || ||||| || || ||||||||||||||||| |||||||
-----------------------------------------gtgcgctcctg-gcgcggtttcttgtggattttgatccggggggtgtgt--tcttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG
upper sequence: GLYMA09G17040.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ35077 (Selaginella moellendorffii), 3'ss of exon 1
agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttcaaattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
||| | | | | | || | | || | | | ||| ||||||||||||||||||| ||||| |||||||| ||||||||||| || ||||||||||| || || ||||| || || ||||||||||||||||| |||||||
-----------------------------------------gtgcgctcctg-gcgcgatttcttgtggattttgatccggggggtgtgt--ttttgcagGCTGGATTTGCCGGAGACGATGCTCCCAGGGCCGTGTTTCCCAGCATTGTGGGCCGGCCCAAGCACACGGGCGTCATGGTTGGAATGGGGCAGAAGGATG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatacaaagagagaactaattgggtgagtacttcaaattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
aactaat putative branch site (score: 2)
aaattatgttcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agttttgtcttttggtttttgatgatactagattttgacccgtgggatacaaagagagaactaattgggtgagtacttcaaattatgttcaattttgcagGCTGGATTTGCTGGAGATGATGCTCCAAGGGCCGTGTTCCCTAGCATTGTGGGTCGTCCACGCCACACTGGTGTGATGGTTGGAATGGGGCAAAAGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - cttttgg
- - - - - - - - - -tgatgat
- - - - - - - - - - - - - - - - - ttgaccc
- - - - - - - - - - - - - - - - - - - - - - -gatacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gggtgag