Sequence
atgc intronic sequence ATGC exonic sequencegtactaaagaacttctgaaatttacggattcgagctccaagtatgatattaacttctttttctttttatttgataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
Basic information
species | Glycine max |
transcript | GLYMA14G02200.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g40840.1 (Oryza sativa), 3'ss of exon 6
gtactaaagaacttctgaaatttacggattcgagctccaagtatgatattaacttctttttctttttatttg-ataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
|| | || || | | | || || || || | || | | | | |||| |||||||||| | |||||||| || || |||||||| ||||| || ||||||||||| ||||| ||||| | ||| | || || ||||| |||| ||||| |
--gttaggagattttc----ttctcaaagtgctcctaggagaatagcataatattttgtctgacatgttttgcgctccaaagGCTGAACTTGAAGTTGAAAGGCTGGATCAGCTCAAAGCTAGTAGGATGAAGGATATTGCGTTCAAAAGGCAGACTGAACTTGAAGATATATATGCCCAGG
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os06g20370.1 (Oryza sativa), 3'ss of exon 6
----------gtactaaagaacttctgaaatttacggattcgagctccaagtatgatattaacttctttttctttttatttgataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
| |||| || || || | | || | | | || || | || || | ||||||| || || ||| | || || || ||||| ||| ||||| |||||||||||| ||||||||||||||| | ||| | ||||| || | ||| |||
gtgagattaaacagtaaatcttttttggtgcaattactgtctgacactaatccttccactgcatttgactttctgtttccaaattgttcagGCTGAGGTAGAGGTTCAAAGGCTAGACCAGCTAAAATACAGCAAGATGAAGGAAATAGCTTTCAAGAAGCAAACTGAGTTGGAAGACATCTATGCTGGTG
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G101874_T01 (Zea mays), 3'ss of exon 7
-------gtactaaagaacttctgaaatttacggattcgagctccaagtatgatattaacttcttt----ttctttttatttgataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
|| ||| | || || | | | |||||| || | | || || || || | ||||||| || || ||| | || | || ||||||||| ||||| |||||| ||||||||||||||||||||| | ||||| ||||| || | || |||
gtgagtcttagtaattattttttggtgctatca---cctgatatgaagtattcctttggcctgcttgacatttacttctccatattgttcagGCTGAGGTTGAGGTTCAAAGGTTAGACCAGCTGAAATACAGCAAGATGAAAGAAATTGCTTTCAAGAAGCAAACCGAGCTGGAAGATATCTACGCTGGTG
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G112337_T04 (Zea mays), 3'ss of exon 6
------------------------------------------------------------------------------------------gtactaaagaacttctga-aatttacggattcgagctccaagtatgatattaacttctttttctttttatttg-ataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
| |||||| | | || || | ||| || | || | | | || | | | ||| | | ||||| ||| | |||||||| || ||||||||||| ||||| || ||||||||||| ||||| |||||||| || | || || ||||| |||| |||||| |
gttagaaactggtttcttttcagagtgttcattggtcttgttaaatactccctccgttctcgaatatttgtcgcccgctagttcatttttgaactaaaacgtgacaaataaaaaactggagggagtaacat-tctgttgtctgtgtgttaataactctccttgcactttcaagGCGGAACTCGAAGTTGAAAGGCTTGATCAGCTAAAAGCTAGTAGGATGAAGGATATTGCATTCAAGAAACAGACTGAACTTGAAGATATATATGCCCGGG
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 9
lower sequence: AT4G26760.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactaaagaacttctgaaatttacggattcgagctccaagtatgatattaacttcttttt----ctttttatttgataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
||| | | | || ||| || || | | |||||||| ||| ||||| || | | | | |||||||| |||||||| || || |||||||| |||||| | ||||| |||||||||||||| ||||| |||||| ||||||| || ||||||| ||| ||||
gtatcgtaaa---tttgtaatgta-----tcaatcaatgtgtatgataagtactgcttttaaaaatcttctgtgaactcttgaagGCTGAGGTGGAAGTGGATAGGCTTGATCAACTGAAATCTAGCAGAATGAAGGAAATTGCATTCAAAAAGCAATCAGAGCTTGAGGAGATATATGCTCGTG
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 9
lower sequence: AT5G55230.1 (Arabidopsis thaliana), 3'ss of exon 6
gtactaaagaactt-ctga--aatttacggattcgagctccaagtatgatattaacttctttttctttttatttgata---ataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
||| | | | ||| ||| | | || ||| || | ||| | | | || || | | | | |||||||| ||||||||||| || ||||| ||||||||||| ||| | ||||| |||||||| |||||||||||| | ||||| |||||||||| ||| ||||
gtaatttatattgcattgatcaatcttcctatgtcctctcttagaaaccagttactgcttgctaatattcatgtaaaatttgtgaagGCTGAGGTGGAAGTTGATAGGCTTGACCAGCTGAAAGCTAGCCGAATGAAAGAAATTGCGTTCAAGAAGCAATCTGAGCTTGAAGAGATATATGCTCGTG
upper sequence: GLYMA14G02200.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv19s0090g01230.t01 (Vitis vinifera), 3'ss of exon 5
---------------------gtactaaag---aacttctgaaatttacggattcgagc----tccaagtatgatattaacttctttttctttttatttgataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
| || || |||| ||| || | || | | | | | |||| | || ||| |||| ||| | |||||||| ||||||||||| || |||||||| ||||||||||||||||||||||||||||||||||||| |||||| |||||||||||||||||||||||||
gtatttggcttcagaacagtaatgcttaattttggcttcagaatagtaatgtttaatggataatgctggcagtttattcattttactttgttttccttttgttgctaagGCTGAGGTGGAAGTTGAAAGGCTTGATCAACTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAGGCAAGCTGAGCTCGAAGAGATATTTGCCCGTGMapped 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|208322033|gb|GE121318.1|GE121318EST: TTGATGAAGTCACTGTTCCTGGTGCCCTTGCTCTGGATCTGATTGAGCAG GCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAG
genomic: TTGATGAAGTCACTGTTCCTGGTGCCCTTGCTCTGGATCTGATTGAGCAGgtactaaaga ... gataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAG
EST:
gi|19934740|gb|BQ079770.1|BQ079770EST: TTGATGAAGTCACTGTTCCTGGTGCCCTTGCTCTGGATCTGATTGAGCAG GCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAG
genomic: TTGATGAAGTCACTGTTCCTGGTGCCCTTGCTCTGGATCTGATTGAGCAGgtactaaaga ... gataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gattcgagctccaagtatgatattaacttctttttctttttatttgataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
cttctttttcttttta CT-rich tract
tatgatattaacttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactaaagaacttctgaaatttacggattcgagctccaagtatgatattaacttctttttctttttatttgataataaagGCTGAAGTGGAAGTTGAGAGACTTGATCAGCTGAAAGCCAGCAGGATGAAGGAAATTGCTTTCAAGAAGCAAGCAGAGCTCGAAGAGATATTTGCCCGTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA