Sequence
atgc intronic sequence ATGC exonic sequence...ttctaaaaaattatgcagagttttcaaatatgtgaattgttctttttggccttggtttgacaaagatttgagaatgattatgtcacatgtaacatggcagGGTCCAGAGATCAGAACTGGGTTTTTGAATGAAGGGAAGCCAATACAAATCCATAGGGGACAAGAAATCACAATCACAACTGATTACAGCATAAAGGGTG
Basic information
species | Glycine max |
transcript | GLYMA16G26830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G003883_T01 (Zea mays), 3'ss of exon 1
------ttctaaaaaattatgcagagttttcaaatatgtgaattgttctttttggccttggtttgacaaagatttgagaatgattatgt-cacatgta-acatggcagGGTCCAGAGATCAGAACTGGGTTTTTGAATGAAGGGAAGCCAATACAAATCCATAGGGGACAAGAAATCACAATCACAACTGATTACAGCATAAAGGGTG
| | | | || | ||| | || | | |||||| || | | || | | | | ||| | || || | || ||||||||||||||| |||||||| |||||||| || |||||||| || ||| | | || |||||||||||||| | || || || ||||| ||||||
ggattatcccatgtacgtagaaacagtactggaa-acat-aattgtgctatgcaaatgtatactggc------ctcatatccattgcatgtactgatatatattgcagGGTCCAGAGATTAGAACTGGATTTTTGAAAGATGGGAAGCCTATTCAATTGATAAAAGGCCAAGAAATCACAATTTCTACAGACTATAGCATTCAGGGTG
upper sequence: GLYMA16G26830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv08s0007g07600.t01 (Vitis vinifera), 3'ss of exon 1
ttctaaaaaattatg--cagagttttcaaatat-gtgaattgttctttttggccttggtttgacaaagatttgagaatgattatgtcacatgtaacatggcagGGTCCAGAGATCAGAACTGGGTTTTTGAATGAAGGGAAGCCAATACAAATCCATAGGGGACAAGAAATCACAATCACAACTGATTACAGCATAAAGGGTG
|| | | || | || |||| || | | | || ||| ||| | ||| | | ||||||||||||||||||||| | ||||| |||||||| || |||||||| | ||| || | | ||| ||||| ||||| ||| | ||||| || ||||| |||||||
agctgacctttcttggtccgaagcaggggatattaccaaaaatattccagagaattccttttttttttttttttttttaatttggatgta---aacatggcagGGTCCAGAGATTCGTACTGGATTTTTGAAGGATGGGAAGCCTGTCCAACTCAAAAAGGGTCAAGAGATCACCATCTCCACTGACTATAGCATCAAGGGTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttggccttggtttgacaaagatttgagaatgattatgtcacatgtaacatggcagGGTCCAGAGATCAGAACTGGGTTTTTGAATGAAGGGAAGCCAATACAAATCCATAGGGGACAAGAAATCACAATCACAACTGATTACAGCATAAAGGGTG
atgtaac putative branch site (score: 3)
aatgattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctaaaaaattatgcagagttttcaaatatgtgaattgttctttttggccttggtttgacaaagatttgagaatgattatgtcacatgtaacatggcagGGTCCAGAGATCAGAACTGGGTTTTTGAATGAAGGGAAGCCAATACAAATCCATAGGGGACAAGAAATCACAATCACAACTGATTACAGCATAAAGGGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - aaaaaat
- - - - - -tatgcag
- - - - - - - - - - - - - - - - - - - - - - - -ggccttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cacatgt