Sequence
atgc intronic sequence ATGC exonic sequence...aatgacacccctagttgcctgtgtactttctcagcccaggttttacagcattgacataatttgtcaggcatatgaatgaaagcttaccatgttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA
Basic information
species | Glycine max |
transcript | GLYMA20G28200.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G176546_T01 (Zea mays), 3'ss of exon 9
------------------------------------------------------aatgacacccctag------ttgcctgtgtactttctcagcccaggttttacagcattgacataatttgtcaggcat-atgaatga---aagcttaccatgttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA
|| ||| | ||| | ||| || || | | | | | | || || || || |||| || || | || || |||||| ||||| || || ||||| || ||||| || ||||| ||||| |||||||||||||| || |||||||||||||| || | || ||||| ||| ||
gtaaaaacgtgcactgttttatattttatccattcagaacttgtgttcttgcagaacacttttccttggctatattgttgatttacattttccctaggcgctgtttgatctcaccgtttttcttcctatattattaatgccttaaatttctcctgg-attttagGAAAAAGAACATTTTCAAGTTAGCTCAAGGAGAATACATAGCTCCAGAGAAGATTGAAAATGTCTATGCCAAATGCAAGTTCATTGCCCAATGTTTTATA
upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 18
lower sequence: AT3G05970.1 (Arabidopsis thaliana), 3'ss of exon 18
----aatg-acacccctagttgcctgtgtactttctcagcccaggttttacagcattgacataatttgtcaggcatatgaatgaaagcttaccatgttgttg-tagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA
| || | | | ||||| | || || | | | | || | || | | | | | ||| ||| ||||| || || | | ||| |||||||| ||||| || ||||| || |||||||| || ||||| ||||| ||||||||||| |||||||||||||||||||||| || ||||| ||
agggagtgcaaagctctagt--cttgggttacattttgg---ggacttgttggtatct-tttgaatcgcgaatcatctgagtgaaattttctgatcctttgaatagAAAGAAGAACATCTTCAAATTGGCGCAGGGGGAGTATATAGCTCCAGAGAAAATTGAAAACGTCTATGCCAAATGCAAATTTGTGGGCCAGTGCTTCATA
upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv05s0020g03080.t01 (Vitis vinifera), 3'ss of exon 18
------------------------------------------------------------------aatgacacccctagttgcctgtgtactttctcagcccaggtttt-----------------acagcattgacataatttgtcaggcatatgaatgaaagcttaccat-----gttgttgta-----gGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA
||||| | | || ||| | | | || | ||| || | | ||||| || | | | | ||||| || |||||| || |||||||||| || ||||||||||||||||| |||||||| ||||| ||||| ||||| || |||||||| |||||||||||||| || || |||||||||
gtaaagaccatatcatttttgttgacagttcttagacgaattaataatgactcctctctagttttggatgactcaattgactgtatgttcatatcttggtcctgtgattttgttattgatataatcgactataattacatacttcattacctgtgcatttcttagctttgtattaaaagttgttatatgacagGAAGAAGAACATTTTTAAGTTGGCACAAGGAGAGTACATAGCTCCAGAGAAAATTGAGAATGTATATGCTAAATGCAAATTTGTTGCCCAGTGCTTTGTA
upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 18
lower sequence: PP1S408_23V6.1 (Physcomitrella patens), 3'ss of exon 20
---aatgacacccctagttgcctgtgtactttctcagcccaggttttacagcattgacataatttgtcaggcatatgaatgaaagc--ttaccatgttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA
||| | || | |||||| |||| | | | || | | || | ||| | | | | | | | | || ||| |||||||||||||||||||||||||| ||||| ||||||||||| || |||||||| || || || || | || | | || || | ||
tgtcgtgagtggatcaatttagcttttactttttcag----gaatgttcacaagtagtatgttctgttcttcgtgtttgttgagtcattcatcacac-attgcagGAAGAAGAATATCTTTAAGTTGGCTCAAGGAGAGTACATTGCCCCGGAGAAGATCGAGAATGTCTACCTTCGCAGTCGTTTCATAACACAGTGTTACATA
upper sequence: GLYMA20G28200.1 (Glycine max), 3'ss of exon 18
lower sequence: PP1S33_126V6.1 (Physcomitrella patens), 3'ss of exon 21
------------------------------------------------------------------------aatgacacccctagttgcctgtgtact----ttctca-gcccaggtttta---cagcattgacataatttgtcaggcat-atgaatgaaag---cttaccatg-ttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA
| || ||||| | ||| || |||| | | | | | || | |||| ||| || || | |||| | | ||| || || || ||| || |||||||||||||| |||||||| || || ||||||||||| || ||||||||||| ||||| || | | || | || || |||||| |
gtactctggactagcgtcacccttagatgtatgctattgatatttttcatcattcaacgtctggtagtctagatcagtgtacccagttgagtatgttctactcttctaatgttcgaagatcaatccaactttga-atatttcaggagctttcatgagttgtacgttctttccttggttattgcagAAAGAAGAATATCTTCAAGTTGGCTCAGGGAGAGTACATTGCGCCCGAGAAGATTGAGAACGTCTACCTGCGAAGTCGGTTCATTGCACAGTGCTTTATTMapped 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|151400349|gb|EV270163.1|EV270163EST: GGAGATATTGGGACATGGTTACCTGGTGGTCGTCTCAAAATTATTGATAG GAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAA
genomic: GGAGATATTGGGACATGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtgagatagc ... gttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAA
EST:
gi|6481851|gb|AW201122.1|AW201122EST: GGAGATATTGGGACATGGTTACCTGGTGGTCGTCTCAAAATTATTGATAG GAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAA
genomic: GGAGATATTGGGACATGGTTACCTGGTGGTCGTCTCAAAATTATTGATAGgtgagatagc ... gttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cagcattgacataatttgtcaggcatatgaatgaaagcttaccatgttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA
agcttac putative branch site (score: 3)
acataattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatgacacccctagttgcctgtgtactttctcagcccaggttttacagcattgacataatttgtcaggcatatgaatgaaagcttaccatgttgttgtagGAAGAAGAATATCTTTAAGTTGGCACAAGGGGAGTACATTGCTCCTGAGAAGATTGAAAACGTATATGCCAAATGCAAATTTGTGGCGCAATGCTTTGTA
- -gacaccc
- - - - - - - - -cctgtgt
- - - - - - - - - - - - - - - -cagccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttacc