Sequence
atgc intronic sequence ATGC exonic sequence...aagttttctgtgctctttacatgtgtgtgtcttttaattaatttacctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
Basic information
species | Glycine max |
transcript | GLYMA13G31550.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os02g58090.1 (Oryza sativa), 3'ss of exon 6
------aagttttctgtgctctttaca----tgtgtgtgtcttttaattaatttacctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
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gtaacttgattatctcgattcttttaggcttttcttgggacatgataccagcttactttaggagctg-tgtggtgctcgaattttattta--aatttctttttttttcagGCATATATTGAGAAGGAGGATAGTAAAAAGTTGAAACAAAAGCAGCGGGAGCGTATGCAACCAAAAATGGGCAAGATGGATATAGATTATCAG
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G121354_T01 (Zea mays), 3'ss of exon 2
-----------------------------------------aagttttctgtgctctttacatgt-gtgtgtcttttaattaatttacctaaatcattgctgtagtcgct-gttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
| ||| | | ||| ||| | | | || || | | | | ||| | || | | |||||| | | | ||||| |||||||||||||||||||| |||||| ||||||| || || ||||||||||||| || |||||||| |||||||||||||||||||||
gtaacttgcttcttgtatctcagtaatttacttctttctctgcttattcatttttttttctttgtagagcgctgcggaactattcattccagtttggtgccatgatcatgagctacctaattgatttctaaatgtgtacacagGCGTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGGGAGCGCATGCAGCCCAAAATGGGCAAAATGGATATAGATTATCAG
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G132060_T01 (Zea mays), 3'ss of exon 5
--------------------------------------------aagttttctgtgctctttacatgtgtgtgtcttttaattaatttacctaaatc-attgctgtagtcgctg-ttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
|| || | ||| ||| || | ||| | | | | || || | | |||| | | | |||||||||||||||||||||||||| |||||| ||||||| || || | ||||| ||||| || || ||||| |||||||||||||||||||||
gtaacttgcttctggtatctcagtaatctacctctccctctctctgcttatccaatttttttcttggtggaacactgcagaactattgatatcagtttggtggcataaacatgaaccgcctgattgatttctaaatgtatacacagGCTTATATTGAGAAAGAGGATAGCAAGAAGTTGAAACAGAAACAGCGTGAGCGTATGCAGCCCAAGATGGGCAAAATGGATATAGATTATCAG
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: AT4G21660.1 (Arabidopsis thaliana), 3'ss of exon 5
aagttttctgtgctctttacatgtgtgtgtcttttaat-taatttacctaaatcattgc-tgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
|| | || | ||| | ||| ||| | | || || | || |||| ||||| | | || | ||| ||| ||||||| ||||||||||| ||| ||||||| |||| ||||||||| ||||| | ||||||||||||||||| || ||||| || || || |||
----------------gtaaaagttattctctatcaatataaggtgc--aagtcgctaaatgcttctactgtcagctaattcttgtgtggt-tcttatgtagGCTTACATTGAGAAAGAAGATGGTAAGAAATTGAAGCAAAAGCAACGGGAGAGAATGCAACCAAAAATGGGAAAGATGGACATTGACTACCAG
upper sequence: GLYMA13G31550.2 (Glycine max), 3'ss of exon 6
lower sequence: PP1S505_13V6.1 (Physcomitrella patens), 3'ss of exon 6
--aagttttctgtgctctttacatgtgt-gtgtcttttaattaatttacctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
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tctatatttggaaattcaatctggactcagcatctttagacataacggccctactttgtgttatg--ccatgtatttaatattttatcttatgggctat-cagGCTTATATTGAAAAGGAAGACAGCAAGAAGCTTAAGCAAAAGCAGAGGGAAAAGATGCAGCCAAAGATGGGGAAGATGGACATAGATTATCAGMapped 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|7234841|gb|AW570174.1|AW570174EST: TTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAG GCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCGAAGGGAG
genomic: TTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAGgtaatatgat ... tctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAG
EST:
gi|23725417|gb|BU760662.1|BU760662EST: TTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAG GCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAG
genomic: TTCAGCTTCCTGATTTCATTGCTGCCACTGGAATTGAGAAAATCAGACAGgtaatatgat ... tctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
ttttaat putative branch site (score: 3)
ttgtctc putative PPT
ttttttaattgtcata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aagttttctgtgctctttacatgtgtgtgtcttttaattaatttacctaaatcattgctgtagtcgctgttttttaattgtcatatgttgtctcatgcagGCTTATATTGAGAAAGAGGATAGTAAGAAGCTGAAACAAAAGCAAAGGGAGCGCATGCAACCAAAAATGGGGAAAATGGATATAGATTATCAG
- - - tctgtgc
- - - - - - - - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catatgt