Sequence
atgc intronic sequence ATGC exonic sequencegtatgaagattacacaaatttttgttaaggccagtggcctttgatttttctttcctgaaatgaggatgtgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
Basic information
species | Glycine max |
transcript | GLYMA15G41040.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv19s0027g01670.t01 (Vitis vinifera), 3'ss of exon 4
gtatga-agattaca-caaatttttgttaaggccagtggcctttgatttttctttcctgaaatgaggatgtgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
|||||| | || | | ||||| | | | | || |||| | |||| || | ||| | | ||||||||| |||||||| |||||||||||||||||||| || |||||||| || || || || ||||||||||||||||| || || || ||||| ||||| |||
gtatgatgggttgcttcttttttttatgcacgttattgttctttcttccttctcatcttgacctgggaagcggcatgcagACTGCGGACATCTCTTTGCTTGCAATTTAAGCCCCACCACATTGCGGCAGGTGCAATTTTCCTTGCTGCCAAGTTCCTCAAAGTAAAGCTCCCATCAGAT
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S119_132V6.2 (Physcomitrella patens), 3'ss of exon 7
----------------gtatgaagattacacaaatttttgttaaggccagtggcctttgatttttctttcctga-aatgaggatgtga-----tatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
|| || | | || |||||| | | | || | | | | ||| | ||| | | ||||| || || ||||||||||| | ||||||||||||||||| ||||| || || || || ||||| ||||| ||||||||||||||||| | || |||
caaaaaacttttcagagtttgccagtgaacgaatattttgtagaaagtacttcccctctgtataaggaaagggctgatgggagtgtaaattattgtgcagTCTCCGCACATCACTTTGTCTACAATTTAAGCCTCATCATATTGCTGCGGGGGCTATCTTCCTGGCTGCTAAGTTTCTGAAGGTGAACTTGCCTGAGGAA
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S264_33V6.3 (Physcomitrella patens), 3'ss of exon 5
---------------gtatga-agattacacaaatttttgtt-aaggccagtggcctttg--atttttctttcctgaaatgagg---atgtgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
||| | | |||||| || |||| || | || | ||| | | | |||| ||| | | | | ||||| ||||| ||||| | ||| ||||||| ||||||||||| ||||| || ||||| || ||| | |||||||||||| |||| ||||| || || |||
ttagagatttgccaggtaagctatattacagaagaacatgtttaatgagcatgtctgttgcaagtgagaatagctgaggcaaggggaaagggttgtgcagTCTTCGCACATCGTTGTGCCTGCAATTCAAGCCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAGTTTTTGAAAGTGAATCTGCCCAAAGAT
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S80_193V6.1 (Physcomitrella patens), 3'ss of exon 4
---------------gtatga-agattacacaaatttttgtt-aaggccagtggcctttg--atttttctttcctgaaatgagg---atgtgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
||| | | ||||| || |||| || | || | ||| | | | |||| ||| | | | | ||||| ||||| |||||||| ||| ||||||| ||||||||||| ||||| || ||||| || ||| | |||||||| |||||||| ||||| ||||| |||
ttagagatttgccaggtaagctatgttacagaagagcatgtttaatgagcatgtctgttgcaagtgagaatggctgaggctaggggaaagggttgtgcagTCTTCGCACATCACTGTGCCTGCAATTCAAGCCTCATCATATTGCTGCGGGAGCTATCTTCTTGGCTGCCAAATTTCTGAAAGTGAACCTACCCAAAGAT
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S86_187V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------gtatgaagattacacaaatttttgttaaggccagtggcctttg-atttttctttcctgaaatgaggatg--tgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
| | |||||| ||| || | | | ||| || || | | || | | ||| || | | | ||||||||| || ||||||||| |||||||||||||||| ||||| || || ||||| || ||||| ||||| |||||||| || ||||| || || |||
caagatgccacttttagagatcagcagattaatgttctttgtgctgaaaactgtgaccactgtagtcggaaaggctaatgtaagggtgattattgtccagACTTCGCACGTCACTTTGCCTGCAATTTAAGCCTCACCACATCGCTGCGGGAGCTATCTTCCTCGCTGCTAAGTTTCTCAAAGTGAATCTGCCGAAGGAG
upper sequence: GLYMA15G41040.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ27727 (Selaginella moellendorffii), 3'ss of exon 4
------------------gtatgaagattacacaaatttt---tgttaaggccagtggcctttgatttttctttcctga----aatga------ggatgtgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
||| ||| | | | | |||| | | ||| ||| || | | || ||||| ||| | ||| ||||| || || ||||| || ||| |||| || ||||| || ||||| || ||||| ||||| ||||| ||||| |||||||| ||||||||||| || |||
gtaagctctcgcacaccagtaggaacttcagtctcgactggagtgttggagtccgtgttgtttcatcactttgatgagatgggaatgaagcagtggaagggatgtgcagGCTACGCACATCGCTCTGCCTGCAGTTCAAGCCGCACCACATCGCCGCTGGTGCCATTTTCCTGGCTGCAAAGTTTCTTAAGGTGAAGCTGCCGATCGATMapped 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|120530094|gb|EH258228.1|EH258228EST: GTTGCTCAAAATGCCCTTGCTCAAGTTGCGTGGAATTTTGTAAATGATGG ACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGG
genomic: GTTGCTCAAAATGCCCTTGCTCAAGTTGCGTGGAATTTTGTAAATGATGGgtatgaagat ... tgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttaaggccagtggcctttgatttttctttcctgaaatgaggatgtgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
ctttgat putative branch site (score: 5)
tttgatttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaagattacacaaatttttgttaaggccagtggcctttgatttttctttcctgaaatgaggatgtgatatgcagACTTCGGACATCACTTTGCTTGCAATTTAAGCCTCATCACATTGCAGCTGGAGCCATATTCCTTGCTGCCAAGTTTCTGAAGGTGAAGCTACCATCGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC