Sequence
atgc intronic sequence ATGC exonic sequence...gtttgaccattgctattatacgaataagacctgtcatgcactgttgcttcttaattgcattgatgttaatgtcttgcttgcattttgacctactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA20G34940.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g55360.4 (Oryza sativa), 3'ss of exon 5
gtttgaccattgctattatacgaataagacctgtcatgcactg--ttgcttcttaattgcattgatgttaatgtcttgc--ttgcattttgac-ctact-gtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
| | |||||| | || | | || | | || | | || | | || | | || | || | | ||||| |||||||||| | || || | || ||||| ||||| ||||||||||| ||| | ||||| ||||| |||| ||||| ||| |||| |||||||||||||||
------cttgtcatattatgtgcatgctatttatctagaaacagattacattatagacaccatttgacaaactccatataattcctttgtaatgctacttacacagGTTTCTGTTGCCTGCTTCTCTCATTGTGATTAACGACATTGCTGCCTATCTATTTGGGTTCTTTCTTGGGAGAACACCTCTGATCAAGTTATCTCCAAAG
upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G62430.1 (Arabidopsis thaliana), 3'ss of exon 5
--gtttgaccattgctattata-cgaataagacctgtcatgcactgttgcttcttaattgcattgatgttaatgtcttgcttgcattttgacctactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
| || | | | | ||| | | | || || ||| | | | || || | || | |||| ||| | ||| | || | | | | ||||||||||||||||||| | | ||| | || || ||||| || || || || |||||||||||||||||||| ||||| || ||| | |||||||||
cagactgttcttaacaaacatagcttcttacacttg-catctattttacttttttcttcgctgtaatgtaaattgtctactt--ctgatggcttccaatgcagGTTTCTTCTCCCAGCATCTTTAATTATAATCAACGACATCTTCGCCTACATTTTCGGTTTCTTCTTTGGAAGAACGCCTTTAATAAAGCTGTCTCCAAAG
upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G22340.3 (Arabidopsis thaliana), 3'ss of exon 4
----------------------gtttgaccattgct-attatacgaataagacctgt--catgcactgttgcttcttaattgcattgatgttaatgtcttgcttgc-attttgacctactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
| || ||| | | | || | ||| || || ||| |||| || ||| | || | || || || |||||||||||| || ||| ||||||| ||||| |||||||| ||| ||||||| ||||||||||||||||||||| || ||||| |||||||| ||||||
gtagtcacctattccttttaacgcttcttacttgtttgctccgtgtttagttcttgtgttattttctcttgtatcttggttatgacctgactaaaagtctatttactatactggttgctggtgcagGTTTCTTCTTCCTGCATCACTTATCGTCATCAATGACATATTTGCATATATCTGTGGTTTCTTCTTTGGAAGAACACCGTTGATCAAGTTATCACCAAAG
upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0187g00380.t01 (Vitis vinifera), 3'ss of exon 5
gtttgaccattgctattatacgaataagacctgtcatgcactgttgcttctt---aattgcattgatgttaatgtcttgcttgcattttgacctactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
||| | | ||| || | || || | ||| |||| |||| | |||| || | | ||| | | | |||||||||||| |||||| |||||||||| || ||||| |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||||
-aaggactttgccctttacttgattcttgagtgat-tggattgtcaagtctttggaattctttatttgtttattttcctgacatagtttagtat-caatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACACCTTTGATTAAGTTATCTCCAAAA
upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0598g00010.t01 (Vitis vinifera), 3'ss of exon 5
gtttgaccattgctattatacgaataagacctgtcatgcactgttgcttctt---aattgcattgatgttaatgtcttgcttgcattttgacctactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
||| | | ||| || | || || | ||| |||| |||| | |||| || | | ||| | | | |||||||||||| |||||| |||||||||| || ||||| |||||||||||||||||||
-aaggactttgccctttacttgattcttgagtgat-tggattgtcaagtctttggaattctttatttgtttattttcctgacatagtttagtat-caatgcagGTTTCTTCTTCCAGCATCACTTATTGTTATCAATGATATTGCTGCTTATATCTTTG--------------------------------------------
upper sequence: GLYMA20G34940.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv00s0598g00010.t01 (Vitis vinifera), 3'ss of exon 6
gtttgaccattgctattatacgaataagacctgtcatgcactgttgcttcttaattgcattgatgttaatgtcttgcttgcattttgacctactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
| | || | | || || || || | | || |||||| ||| | || |||| ||
--------------------------------------------------------gtttcttctttggaagaacacctttgattaagttnnnnnnnnnnnnnnnnnncccaagtaaaaactgttttcatta--gac-tagCAACTTACTACTCG---------------------------------------------Mapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|151412323|gb|EV282135.1|EV282135EST: TTTGGCCAGTCCTCCTTCACTGTGGCAAGCATTTTTGAAGGGATTTTCTG GTTTCTTCTCCCAACAACACTTATTGTCATTAATGACATTGCTGCTTATAT
genomic: TTTGGCCAGTCCTCCTTCACTGTGGCAAGCATTTTTGAAGGGATTTTCTGgtaatataac ... tactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATAT
EST:
gi|193626812|gb|FK578370.1|FK578370EST: TTTGGCCAGTCCTCCTTCACTGTGGCAAGCATTTTTGAAGGGATTTTCTG GTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATAT
genomic: TTTGGCCAGTCCTCCTTCACTGTGGCAAGCATTTTTGAAGGGATTTTCTGgtaatataac ... tactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcttcttaattgcattgatgttaatgtcttgcttgcattttgacctactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
ttttgac putative branch site (score: 3)
atgttaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgaccattgctattatacgaataagacctgtcatgcactgttgcttcttaattgcattgatgttaatgtcttgcttgcattttgacctactgtacagGTTTCTTCTCCCAGCAACACTTATTGTCATTAATGACATTGCTGCTTATATCTTTGGTTTCTTCTTTGGAAGAACCCCTTTGATTAAGTTATCTCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - ccattgc
- - - - - - - - - - - - - - - - - catgcac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttgca