Sequence
atgc intronic sequence ATGC exonic sequence...gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcggtttcttatatcaatttctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
Basic information
species | Glycine max |
transcript | GLYMA17G00480.1 |
intron # | 18 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 3'ss of exon 18
--------------------gcttttttagaaggtacaaacatgaaccaattt--acagtccatctagaattcactttcggtttcttatatcaatttctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
|| || | || || || | |||| |||| | | || | | | | || ||| | | | | | | ||| |||| |||||| || || || | |||||| ||||| ||||| | |||||| ||||||||||||||||| ||||| ||||||||||| | ||| ||||| |
gtaagtcagaatccttcttttattcttcaaaaagttcat-cgtgaaaagattttgaaaatcatcttctagagtagaaaggattaattagtatatcgtttttgtaatcctttcctattttcagGACACGATGCTTAGAAAGCCAGTAGATCCTGAGGAAGAGCTTAAATGGATATCTCAAGAAGTCCGTGGGTATGTGGAAGCTGTTCTCAGCAGTCTTGCGG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 18
-gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcggtttcttatatcaattt-ctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
|| ||| | ||| || | | | ||| | | |||| | ||| | |||||| | | | | | |||||||||||| ||||| ||| |||||| ||||| || || || || ||||||||||| || ||||| |||||||||||||| |||||| | || || || ||||
atgttccttaagataaacatgt-tgtattgttgttgttggcatgagttacttacttcca-tttgacctttcaattgacatctgatccctgcacttttcaaagGATACTATGGCACGGAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 3'ss of exon 18
gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcg---gtttcttatatcaatttc----tccatgttgcaaaatcattca-----aagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
|| ||| || ||| ||| | | | | ||| ||| | || || | | ||||| | | ||| || ||| | || ||||||||||||||| |||| ||||| ||||| || || || || | ||||||||||||||||| ||||||||||| || |||||| | ||||| | ||||
----------ctcatatcaacctgttccactttccca--cggccatgattattttttgaatgtgtcaaacacaaattttgaattgcctgtgacacaattactctcccttaagGATACGATGGCCCGGAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G870253_T01 (Zea mays), 3'ss of exon 2
----gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcggtttcttatatcaatttctccatgttgcaaaatcattca----aagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
|| |||| || |||| ||||| | | ||| | | | | | ||||| | | ||| ||| | ||| ||| |||||||| ||||| ||| ||||| ||||| || || || || ||||||||||||||||||||||||||||||||||||||||| | ||||| | || |
ttttatcttacctaaaggctaaagcatgttttcattta-aatgtatccaaacacaa-----gatcacttatttta--ctcttcattctacaactcttttctgtttaagGATACAATGGCTCGGAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM5G811223_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------------------------------------------------------gcttttttagaaggtacaaa----catgaaccaatttacagt-ccatctagaattcactttcggtttcttatatcaatt--tctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
| | | | | | || | || | || || ||| ||| | | | | || | || | | | | | | | | ||||||| | ||||| ||| ||| || ||||| || || || || |||||||||||||||||||| |||||||||||||| |||||| | || || || ||||
gtaagttctaggttaatacataattgaattgcatttctagctttccttttgtagttttgctttactcaattaaatcttgatttattagggatcatcatgtaatttcaggttcccttgtatgttttggatgtgccaatataaatactgctccattaaaatacacaaactaaacatctgatcatacacttttcgaaagGATGCTATGGCGCGGAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 18
----------------------------------------------------------------------------------------gcttttttagaaggtacaaa---catgaaccaattt--acagtccatctagaattcactttcggtttcttatatcaattt-ctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
| | | | | | || | | | ||| | ||| ||| || | | || | || | | | | | | | ||||||||| ||||| | | |||||| ||||| || || || || |||||||||||||||||||| ||||||||||| || |||||| | || || || ||||
gtaagttctagattaatacataattgtattgcatttctagctttcttttgtcgttttgctctactcaactaaatcatgatttattaaggatcatcatgtaatttcaggtccccttgtatattttggatgtgccaatataaatatttttccattaaaatacacaaactaacatctgaccatacatttttcaaaagGATACTATGGCACGTAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 3'ss of exon 18
gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcggtttcttatatcaatttctccatgttgcaaaatcat-tcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
|| ||| || | | | | | || ||| | | | | || | | || | | || | | || | | | |||||| ||||| |||||||| |||||||| ||||||||| | |||||||| |||||||| || ||||| ||||||||||||||||||||||||||||
actacttttaaacttg-acataagttatgtttgacatttaaggtttttattgtttataatattttctgagacttacgtttttttccttgtctgtatttcagGATAAGATGGTTAGGAAACCCATCGATCCAGAAGAGGAGCTCCGGTGGATGTCCCAAGAAGTACGGGGTTACGTTGAAGCTGTTCTTAACAGCCTTGCAG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 3'ss of exon 18
------------gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcggtttcttatatcaatttctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
||||| || | | | | ||| | | | | || ||| | || | ||||| | | || |||||| ||||| |||||||| | || || || ||||| | | |||||||| |||||||| || |||||||||||||||||||| ||||| || || |
agggttaagatagctttgtttgggcatgtgag-gcgtttaggtttccggatgggtggtattacagttttgccttggttgtctaattttttt-----------cctttttcagGATAAGATGGTAAGGAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTG
upper sequence: GLYMA17G00480.1 (Glycine max), 3'ss of exon 18
lower sequence: Vv12s0035g01740.t01 (Vitis vinifera), 3'ss of exon 18
gcttttttagaaggtaca-aacatgaaccaatttacagtcca---tctagaattcact-ttcggtttcttatatcaatttctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
|| | || | || ||||| || | || ||| || | | ||| | || ||| | || | | | | | || || | ||||||| |||||||| | |||||| |||||||| || |||||| ||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| |
--ttctgtactggccccagaacataaat---tctatagttcacattttttcatttgttattaggtcttttgtggttactgtttggttgccttgaaaattttatagGATACAATGGCCAGAAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGMapped 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|17400218|gb|BM177000.1|BM177000EST: TTGGTGAACCTAGTTTTCCTATGCGGCAAAGCCTTTCTGATGGGTCTCTT GATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTC-TTTGTATG
genomic: TTGGTGAACCTAGTTTTCCTATGCGGCAAAGCCTTTCTGATGGGTCTCTTgtaagtttct ... tcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATG
EST:
gi|193690156|gb|FK634537.1|FK634537EST: TTGGTGAACCTAGTTTTCCTATGCGGCAAAGCCTTTCTGATGGGTCTCTT GATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATG
genomic: TTGGTGAACCTAGTTTTCCTATGCGGCAAAGCCTTTCTGATGGGTCTCTTgtaagtttct ... tcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gaattcactttcggtttcttatatcaatttctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
tttcttatatcaattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcttttttagaaggtacaaacatgaaccaatttacagtccatctagaattcactttcggtttcttatatcaatttctccatgttgcaaaatcattcaaagGATACGATGGCCAGGAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - caaacat
- - - - - - - - - - - - - - - - - - - ccatcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ccatgtt