Sequence
atgc intronic sequence ATGC exonic sequence...tttcatgggagcttcctgattggattttaattctacaatcattattagaattcaatttgaaacaaggctgctcacttaccaattacttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
Basic information
species | Glycine max |
transcript | GLYMA18G47140.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g06060.1 (Oryza sativa), 3'ss of exon 2
---tttcatgggagcttcctgattggattttaattctacaatcattattagaattcaatttgaaacaaggctgctcacttaccaattacttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
||| || || | | | ||| | | | || | | |||||| | || | || | | || | | ||||| || | | || ||||| ||||| |||||| |||||| |||||||||||||| |||||||| |||||| | ||||| |||||||| || || |
gtcttttatcttggcaatactagggattgttagatgattagatagtaacaagaaacaattttttttgtgacttgtgacaaa--atctagccatttttcacagGTCATCTCAATAAAGGACATCATACGGCCACCAAGGAGGGAGAACTTCAATGATGTCTACATTGTCTATGAGCTCATGGACACTGATCTTCACCACCTTC-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g38950.1 (Oryza sativa), 3'ss of exon 2
tttcatgggagcttcctgattggattttaattctacaat-cattattagaattcaatttgaaacaaggctgctcacttaccaatt-acttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
|| | | || || || | | | || |||| || || || | | | | | | || | || | ||| | || ||| | || ||||| || || || ||| || || ||||| |||||||| |||||||||| |||||| |||||||||||||| ||||| || |
ttccttttttttttgttgggcgg-tcaagagcgtgtgatacatttttgactcacacatttatatcatatagtctgatggtgattttaacactggatcacagATTATTGCCATAAAGGACATAATTCGCCCCCCAAGAAGAGACAACTTTAATGATGTTTACATTGTTTCTGAGTTGATGGATACTGATCTCCATCAGATCA-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G127141_T01 (Zea mays), 3'ss of exon 2
-----tttcatgggagcttcctgattggattttaattctacaatcattattagaattcaatttgaaacaaggctgctcacttaccaattacttctctaat-gcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
| | || | | | || || |||||| ||| | | | ||| | | | | || | | | | || | | | ||| | | ||| | || || | || || || ||| || || ||||| ||||| |||||||||||| ||||||||||||||| ||||| ||||| ||
tatgcatgtgttagaaccatc-aaccatgttgtacttctac--tcagcaatgaagttc--ctatgatctaatttgtctaataatgattttaacttgtggtcacagATCCTTGCCTTAAAGGATGTAATTCGGCCCCCAACTAGAGAGAACTTTAATGACGTGTACATTGTTACTGAGTTAATGGATACAGATCTCCATCAGATCG-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G46070.2 (Arabidopsis thaliana), 3'ss of exon 2
---------------------------------------------tttcatgggagcttcctgattggattttaattctacaatcattat--tagaattcaatttgaa-acaaggctgctcactta-----ccaattacttctctaatgc---aggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
|||| | || || | || | ||| | | | ||| | ||| | | || | | ||| ||| | | || | |||| ||| || | ||||| ||| || |||| || || | |||| |||||||||||| |||||||| |||||||||||||| |||||||| || | |||
gtaagccttaagcatcatttctcacatttgacaacatcttttaagtttctca--aatttgctagatctatcaagtgttcctgatcttcagggtcaaatgctctttatatataatttcgtttactctaatcttcaagcctcggtttgattctttagGTTATAACCATCAAAGATATTGTAAGACCTCCGCAACGAGATATCTTCAATGATGTCTACATTGTCTATGAGTTAATGGACACTGATCTTCAGCGAATCC-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G01560.1 (Arabidopsis thaliana), 3'ss of exon 2
tttcatgggagcttcctgattggattttaattctacaatcattattagaattcaatttgaaacaaggctgctcacttaccaattacttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
| ||||| | |||||| || || ||| | || ||| | || | || | | | || | ||| | ||||| || ||| ||| |||||| ||| ||||||| ||| || |||||||||||||| ||||||| |||||||||||||| |||||||| || || || |
------gtaagctttt--gtcttattttattt-----attattctccacatgt--tttctagtaattatcctgattctggagtt---tatctca--cagGTCATTGCCATTATAGACATAATAAGACCACCTCAGCCAGACAACTTCAATGATGTTCACATTGTCTATGAGTTAATGGACACTGATCTTCACCACATTA-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G01370.1 (Arabidopsis thaliana), 3'ss of exon 2
tttcatgggagcttcctgattggattttaattctacaatcattattagaat-tcaatttgaaacaaggctgctcacttaccaattacttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
| | ||| | || || || || || || | || || || || |||||||||| || | || || || ||| |||||| ||||| || |||||||||||||| ||||||||||||||| | ||||| |||||||| || ||||| |
-------------------------gtacgtgttacta--atcatcagcatctctggttttttttgtgtgaatcttatattggtttatt-----gtgcagGTGATTGCTGTAAAGGATATAATAAAACCACCGCAGAGAGAGAACTTCAATGATGTTTACATTGTTTATGAGCTTATGGACACTGATCTCCACCAAATTA-
upper sequence: GLYMA18G47140.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv15s0046g02010.t01 (Vitis vinifera), 3'ss of exon 2
----tttcatgggagcttcctgattggattttaattctacaatcattattagaattcaatttgaaacaaggctgctcacttaccaattacttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
| | | | | ||||||| ||||| ||| || | || || || || | | ||| | || || ||| || |||||| || | | | |||||||| ||||| ||||| ||||||| |||||||||||||| |||||||||||||| |||||||| |||||||||||||| ||||
ctttagttactttggttcgtttgttggattcaggttctagaattttttatgttcctcctggtggaataata-tatttact-atcagtt-cttatcctccgcagGTTATTGTCTTGAAAGACATCATACGGCCACCTAAGAGGGAGAACTTCAATGATGTCTACATTGTTTATGAATTAATGGACACTGATCTGCATCAGATAA-Mapped 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|15813475|gb|BI785750.1|BI785750EST: AAGGACTCTACGAGAAATTAAACTTCTTCGGCACATGGATCATGAAAATG TGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATG
genomic: AAGGACTCTACGAGAAATTAAACTTCTTCGGCACATGGATCATGAAAATGtaatttaaat ... ctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATG
EST:
gi|151406082|gb|EV275897.1|EV275897EST: AAGGACTCTACGAGAAATTAAACTTCTTCGGCACATGGATCATGAAAATG TGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATG
genomic: AAGGACTCTACGAGAAATTAAACTTCTTCGGCACATGGATCATGAAAATGtaatttaaat ... ctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagaattcaatttgaaacaaggctgctcacttaccaattacttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
ttacttctct CT-rich tract
aatttgaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcatgggagcttcctgattggattttaattctacaatcattattagaattcaatttgaaacaaggctgctcacttaccaattacttctctaatgcaggTGATAGCCCTTAAAGACATTATACGACCACCACAGAGGGATAACTTCAATGATGTGTACATTGTTTATGAGTTAATGGATACTGATCTGCATCAAATAAT
-ttcatgg
- - - - - gcttcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aggctgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacttac