Sequence
atgc intronic sequence ATGC exonic sequence...tttatgatattgctgcaagttagaacatttgacttgaagttattcaaagctttttactggttttcagactttggtttaaacgattaggctgatgtttcagGTTGCACTGGTAGTTGGTGGGGGTAACATCTTCCGTGGATCCTCCTGGGCTGGAAGTAGTGGACTAGACCGCTCATCTGCGGATTATATTGG
Basic information
species | Glycine max |
transcript | GLYMA05G32340.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G32340.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g73450.1 (Oryza sativa), 3'ss of exon 3
tttatgatattgctgcaagttagaacatttgacttgaagttattcaaagctttttact---ggttttcagactttggtttaaacgattaggctgatgtttcagGTTGCACTGGTAGTTGGTGGGGGTAACATCTTCCGTGGATCCTCCTGGGCTGGAAGTAGTGGACTAGACCGCTCATCTGCGGATTATATTGG
| || | | | || | | | | | | | || | | | || | ||||| ||| || || |||||||| | || |||||||| || || |||||||| || |||| ||||||||| |||||||||| ||||||||||| || ||||| |||||
-ctgtgttccaacgaagtggtattatgctatgtgtatgttcctcttgtcttctctattgtagaaacatatgctgtacattaaa-gatcggga-acccttgcagGTTGCTATTGTTGTTGGTGGCGGCAATATCTTCCGCGGGGCCTCTTGGGCTGGATGTAGTGGACTCGACCGCTCATCAGCAGATTACATTGG
upper sequence: GLYMA05G32340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G139462_T06 (Zea mays), 3'ss of exon 3
tttatgatattgctgcaagttagaacatttgacttgaagttattcaaagctttttactgg---ttttcagactttggtttaaacgattaggctgatgtttcagGTTGCACTGGTAGTTGGTGGGGGTAACATCTTCCGTGGATCCTCCTGGGCTGGAAGTAGTGGACTAGACCGCTCATCTGCGGATTATATTGG
| | || | || | || | | ||| | ||| | | || | || ||||| || | | || |||||||| | || ||||| || || || ||||||||||| |||| ||||||||| ||||||| || |||||||||||||||||||| || ||
---caagtgcttttggatgtgtatttgtgtgtgtgtgatttaccttttgttttctctaaagcaatcgcatgatgtgcattaaaaaatgtgagagcccttgcagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTCCGTGGGGCCTCTTGGGCTGGATGTAGTGGGCTTGACCGCTCATCTGCGGATTACATCGG
upper sequence: GLYMA05G32340.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G149535_T01 (Zea mays), 3'ss of exon 3
tttatgatattgc-tgcaagttagaacatttgacttgaagttattcaaagctttttactg-gttttcagac--tttggtttaaacgattaggctgatgtttcagGTTGCACTGGTAGTTGGTGGGGGTAACATCTTCCGTGGATCCTCCTGGGCTGGAAGTAGTGGACTAGACCGCTCATCTGCGGATTATATTGG
|||| ||| || | | || | || || | ||| | || ||| | | || ||||| || | | || ||||||| | || ||||| || || || ||||| ||||| |||| ||||||||| ||||||| || |||||||||||||| ||||| || ||
----tgatcttggatgtgtatctgtactctgtgtgtgtcattgccttttgttttctctaaagtaatcatataatgtgcattaaaacatgtgagagcccttgtagGTTGCTATTGTTGTTGGCGGTGGCAATATCTTTCGTGGGGCCTCTTGGGCTGGATGTAGTGGTCTTGACCGCTCATCTGCAGATTACATCGG
upper sequence: GLYMA05G32340.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0044g00890.t01 (Vitis vinifera), 3'ss of exon 4
tttatgatattgctgcaagttagaacatttgacttgaagttattcaaagcttt-ttactggttttcagactttggt--ttaaacgatta--ggctgatgtttcagGTTGCACTGGTAGTTGGTGGGGGTAACATCTTCCGTGGATCCTCCTGGGCTGGAAGTAGTGGACTAGACCGCTCATCTGCGGATTATATTGG
||| || || |||| | ||| | ||| ||| |||||| || | |||| | |||| | || ||| | |||| ||||||||||| | || ||||||||||| || || || ||||||||||| ||||| |||||| |||| || || || || ||||| ||||| |||||
gttaggacat----gcaatcggacttgtatgaactaaaga-attggaagcttcattgttaactttctttatatggtatcttaatcattgttgatagatgcttcagGTTGCAATTGTGGTTGGTGGGGGAAATATTTTTCGTGGATCCTCTTGGGCAGGAAGTGGTGGCCTTGATCGTTCTTCTGCTGATTACATTGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaagctttttactggttttcagactttggtttaaacgattaggctgatgtttcagGTTGCACTGGTAGTTGGTGGGGGTAACATCTTCCGTGGATCCTCCTGGGCTGGAAGTAGTGGACTAGACCGCTCATCTGCGGATTATATTGG
ggctgat putative branch site (score: 4)
tttttact 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttatgatattgctgcaagttagaacatttgacttgaagttattcaaagctttttactggttttcagactttggtttaaacgattaggctgatgtttcagGTTGCACTGGTAGTTGGTGGGGGTAACATCTTCCGTGGATCCTCCTGGGCTGGAAGTAGTGGACTAGACCGCTCATCTGCGGATTATATTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - -tgcaagt
- - - - - - - - - - - - - - -tgacttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gactttg