Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
Basic information
species | Glycine max |
transcript | GLYMA18G02210.4 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os10g22450.1 (Oryza sativa), 3'ss of exon 9
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaa-aaagttggcaaggttactcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
| ||| ||| || ||| || | |||| || | | | | |||| || ||| ||| | || | || ||||||||| || || |||||||||||||||||| || | |||||| | || |||||||| ||||| ||||||| ||||||||| ||||||| ||||| ||||
------------------------------------------------------------------------------------------------acttgcaggaacaaaacaaatttctgttagtttctgttgcaatgcaatgt-gctgaaaaatcatttgaaattgatgaggagtttggttg-atgaaact-gcagGTTCCCCCAGGCACACCAGTGGTGAATGCACTGGCCAAGCAGAGGGCCATGCTGGAGAACATCCTGAGGGCCTGTGTTGGACTGGCCCCTGAGAACAACA
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g09250.2 (Oryza sativa), 3'ss of exon 9
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttg---cagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
| || || | | || || | | | | || || | | ||| | || | || || | || ||| || |||||||| || || |||||||||||||| || || |||||||| | |||||||| || ||||| |||||||| || ||||| ||||||| ||||| ||||
---------------------------------------------------------------------------------------------------------------gtactgcccattaa----ccgttatgttctttcatgatat----accaactgatttacttatgtcacgaaaaattcgtctcctggaacagGTTCCTCCTGGCACACCAGTGGTGAACGCCCTGGCAAAGCAGAGGGCAATGCTTGAGAACATCATGAGGGCCTGCGTTGGGCTGGCCCCCGAGAACAACA
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: LOC_Os03g09250.3 (Oryza sativa), 3'ss of exon 8
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttg---cagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
| || | | ||| ||| | | ||| || || | | || ||| | | | ||| | || | || || | || ||| || |||||||| || || |||||||||||||| || || |||||||| | |||||||| || ||||| |||||||| || ||||| ||||||| ||||| ||||
----------------------------------------------------------------------------------------------gtgagtgcatacatgcatc--tgtactgcccattaaccgttatgttcttt--catgatat-accaactgatttacttatgtcacgaaaaattcgtctcctggaacagGTTCCTCCTGGCACACCAGTGGTGAACGCCCTGGCAAAGCAGAGGGCAATGCTTGAGAACATCATGAGGGCCTGCGTTGGGCTGGCCCCCGAGAACAACA
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G004528_T03 (Zea mays), 3'ss of exon 9
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtga-atttcccttttttccccttatcatttttttatcaaaaaagttggcaaggtta-ctcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
|| | || | | | |||| | | | ||| || | ||| || | || || || |||| | | ||||||||||| || ||||| |||||||| || | |||||||| | || |||||||| ||||| ||||||||||| ||||| ||||||||||||| ||||
---------------------------------------------------------------------------------------------------------gtaagccttttcgcctgcattaattccggcatcgctgcaccgcatcttgct-ccaatccagccgctaatcttctcttacaaaacctgaatgacagGTTCCACCCGGCACACCGGTGGTGAACGCTCTTGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCTTGCGTTGGCCTGGCCCCAGAGAACAACA
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G145638_T02 (Zea mays), 3'ss of exon 4
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactc--acaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
||| | || | | | || || | | | | || || || | || | | ||| |||| | |||||||| || || ||||| |||||||| || || |||||||| | || |||||||| ||||| |||||||| || ||||| |||||||||||||| ||||
----------------------------------------------------------------------------------------------------------gtaagccttttcgcctgcattaattctggcatcgctgcaccgcatcttgctccaatccaatcgctaatcttctcttacaaaacctgaacgacagGTTCCGCCCGGCACACCGGTGGTGAACGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGCGTTGGCTTGGCCCCAGAGAACAACA
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G392513_T02 (Zea mays), 3'ss of exon 7
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatc-aaaaaagttggcaaggtta-ctcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
||| | || | | | || || | | | | || || || || | || || || |||| | ||||||| || || |||| ||||||||||| || |||||||| | || |||||||| ||||| |||||||| |||||||| |||||| |||||| ||||
----------------------------------------------------------------------------------------------------------gtaagccttttcgcctgcattaattctggcatcgctgcaccgcatcttgctctaatctagccgctaatcttctcttacaaaacctgaacgacagGTTCTGCCCGGCACACTGGTGGTGAATGCTCTGGCAAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGTGTTGGCCTGGCCCTAGAGAACAACA
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G155242_T01 (Zea mays), 3'ss of exon 9
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
|| | || | | | | | | | | | | || ||| | | || | ||| ||| | | |||||||| || || ||||| |||||||| || || | |||||| | || |||||||| ||||| |||||||| || ||||| ||||||||||||| ||||
---------------------------------------------------------------------------------------------------------gtaagccttttctcctgcatcccggcatcactgcactgcgttttgcttcaatccagcca-ctgatcgtctctctcgaaacctgaaca--acagGTTCCCCCTGGCACACCGGTGGTGAACGCTCTGGCCAAGCAGAGGGCGATGCTGGAGAACATCATGAGGGCCTGCGTTGGGCTGGCCCCAGAGAACAACA
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: AT5G10170.1 (Arabidopsis thaliana), 3'ss of exon 9
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
|| ||| ||| | | | | || ||||| | || | || | | || | ||| || || |||||||||| || || || ||||| || ||||| ||||| || |||||||||||||| || ||| || | || |||||||||||| | || || ||||| ||||
----------------------------------------------------------------------------------------------------gt-aagcaaaaccgaagcaaaacattgtgccgtttttcaatcctagcgacttccttt-------------aacatcactttca-ttcaatgaatgcagGTTCCTCCTGGCACGCCAGTTGTTAATGCTTTGTCGAAACAGCGTGCAATGCTTGAGAACGTACTCAGAGCTTGTGTTGGACTTGCTCCTGAGAACAACA
upper sequence: GLYMA18G02210.3 (Glycine max), 3'ss of exon 9
lower sequence: Vv07s0031g00920.t01 (Vitis vinifera), 3'ss of exon 9
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
|| | | | | ||| | | | | |||| | || | || |||| | | | || || | | || | | |||| ||||||||| || || ||||||||||||||| || | |||||||| |||||||| || |||||| | |||||||||||||||||||| || ||||| ||||
-----------------------------------------------------------------------------------gacatcaaagttttaccttcttgtttgg--aatatgcgaggaatgtagagttagttga--tagcattatgatgttgtaacgttttgttggtgtattaaaaaca-----------gGTTCCACCAGGCACTCCAGTGGTGAATGCACTGGCGAAGCAGCGGGCAATGCTCGAGAACATACTAAGGGCTTGTGTTGGATTGGCTCCCGAGAACAACAMapped 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|208315496|gb|GE116190.1|GE116190EST: CATTCCACCCAGTTGCTACCATTCTCAGCTATCTGACCAAGGCTCCTCTG GTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATG
genomic: CATTCCACCCAGTTGCTACCATTCTCAGCTATCTGACCAAGGCTCCTCTGgtgagtttaa ... actcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATG
EST:
gi|193686704|gb|FK626097.1|FK626097EST: TTCCACCCAGTTGGCTACCCATTCTCAGCTATCTGACCAAGGCTCCTCTG GTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATG
genomic: TTCCACCCAGTT-GCTA-CCATTCTCAGCTATCTGACCAAGGCTCCTCTGgtgagtttaa ... actcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATG
EST:
gi|208190804|gb|GD991424.1|GD991424EST: TACCATTCTCAGTCTTATCTGACCAAGGCTCCTCTG GTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATG
genomic: TACCATTCTCAG-C-TATCTGACCAAGGCTCCTCTGgtgagtttaa ... actcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
ctcttgc CT-rich tract
tttttttatcaaaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttaatctaatcttattcaatgttgagtgcatatccttatttttatataggaattaagttgaaagaaatatgagttttagtattgagatacaattgtgaagttaaatcattgttcagtgaatttcccttttttccccttatcatttttttatcaaaaaagttggcaaggttactcacaacataactcttgcagGTTCCACCGGGTACACCAGTGGTGAATGCATTGTCAAAGCAGCGTGCAATGCTGGAAAACATAATGAGGGCTTGTGTTGGATTGGCCCCAGAGAATAACA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA