Sequence
atgc intronic sequence ATGC exonic sequence...gtgcatacatggctggagaatgttattttatgcctgttgttatgtccatttgttattggttgttttcctgggttgattttggccgtattatgacatccagGTTAGATGTGTTGCTTCAGACTTGGAAAGGAAAAGGATATGCAGCGGTGGTCGCAATGGGCTTCTAAGGCTGTGGGATGCAACTATTAATATTTGAGCTT
Basic information
species | Glycine max |
transcript | GLYMA05G35210.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 14
lower sequence: LOC_Os01g39380.1 (Oryza sativa), 3'ss of exon 31
gtgcatacatggctggagaatgttattttatgcctgttgttatgtccatttgttattggttgttttcctgggttgattttggccgtattatgacatc--cagGTTAGATGTGTTGCTTCAGACTTGGAAAGGAAAAGGATATGCAGCGGTGGTCGCAATGGGCTTCTAAGGCTGTGGGATGCAACTATTAATATTTGAGCTT
| || | || | || || | | ||| ||| | ||| | ||| | | |||| | | ||| || | ||||| |||||||| || || ||| |||| ||||||| || ||||||||||||||||| || ||||| |||| |||||||| || | | ||| | || |
gaaaatgcttgtaacaaaaacaaacttagttatacatcgttgtgtttttcctttaat--ttggcatattatgttgttaagtcctcaattttgcttttgacagGTGAGATGTGTAGCATCGGACCTGGATCGGAAAAGAATCTGCAGCGGTGGTCGCAACGGACTTCTTCGGCTTTGGGATGCCACCACGAGTATCTAAGTTA
upper sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 14
lower sequence: AT1G49040.1 (Arabidopsis thaliana), 3'ss of exon 30
----------------------------------------------------------------------------------------gtgcatacatggctggagaatgttattttatgcctgttg----ttatgtcc----attt--gttattggttgttttcctgggttgattttggcc--gtattatgacatccagGTTAGATGTGTTGCTTCAGACTTGGAAAGGAAAAGGATATGCAGCGGTGGTCGCAATGGGCTTCTAAGGCTGTGGGATGCAACTATTAATATTTGAGCTT
| || | | | || | | | || || ||| | | || | || | ||| | || | | | | | ||| || ||||| ||||||||||| ||||| | || |||||| ||||||| |||||||| || ||||| |||| ||||||||||||| || || || || ||| |
gtacgaccctccctcttttcatattagttggatagttgctctaaatttttctggtcatgcggtttgataagtcttatgagatcctgtaacaccctcaaagtagtatgataagaccacacagttattaatcattgtgttctacaacttcggctagtatgtgtcattctcactgaaactgaatctcggatttaatgattcagGTGAGATGTGTTGCGTCAGATCTCGAGAGGAAACGGATATGTAGCGGTGGCCGAAATGGAGTTCTCCGGCTGTGGGATGCCACCATCAACATCTGATTAT
upper sequence: GLYMA05G35210.1 (Glycine max), 3'ss of exon 14
lower sequence: Vv17s0000g03950.t01 (Vitis vinifera), 3'ss of exon 30
gtgcatacatggctggagaatgttattttatgcctgttgttatgtccatttgttattggttgttttcctgggttgattttggccgtat-tatgacat--ccagGTTAGATGTGTTGCTTCAGACTTGGAAAGGAAAAGGATATGCAGCGGTGGTCGCAATGGGCTTCTAAGGCTGTGGGATGCAACTATTAATATTTGAGCTT
| | | | ||| | | | || || | | | || | || | | ||| || |||| | || | | ||||| | |||||| ||||| || |||||||| | ||||| |||||||||||||| |||||||| ||||| ||||| ||||| ||||| || || || || || | || |
--ggctttaagcttggtggtaataaaagtagagaagtatatgtatttatgt-ctactactgatttcagcggattgacacagaccttttatatgatgtgtccagGTAAGATGCGTGGCTTCAGATCTTGAAAGAAAAAGGATATGCAGTGGTGGTCGTAATGGACTTCTTAGGCTATGGGAAGCGACCATCAACATCTAAGTCT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccatttgttattggttgttttcctgggttgattttggccgtattatgacatccagGTTAGATGTGTTGCTTCAGACTTGGAAAGGAAAAGGATATGCAGCGGTGGTCGCAATGGGCTTCTAAGGCTGTGGGATGCAACTATTAATATTTGAGCTT
ggttgat putative branch site (score: 5)
ttgatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgcatacatggctggagaatgttattttatgcctgttgttatgtccatttgttattggttgttttcctgggttgattttggccgtattatgacatccagGTTAGATGTGTTGCTTCAGACTTGGAAAGGAAAAGGATATGCAGCGGTGGTCGCAATGGGCTTCTAAGGCTGTGGGATGCAACTATTAATATTTGAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- gcataca
- - - - -tggctgg
- - - - - - - - - - - - - - tatgcct
- - - - - - - - - - - - - - - - - - -tgttatg
- - - - - - - - - - - - - - - - - - - - - - -ccatttg