Sequence
atgc intronic sequence ATGC exonic sequence...ccactcacaatcatatatatatatatgtctatcagtctacaacaatgatagttttaatacatagatgatgctaacatactttgtgcatgtctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
Basic information
species | Glycine max |
transcript | GLYMA18G47240.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os03g03460.1 (Oryza sativa), 3'ss of exon 2
----ccac-tcacaatcatat--atatatatatgtctatcagtctacaacaatgatagttttaatacatagatgatgctaacatactttgtgcatgtctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
| | | | || | | | | || || || || || | || | | || | ||| | ||||| | | || ||| |||| | ||||||||| || || || || ||||| | ||||||||| ||||||||||| || |||||||||||||| |||||||| || | ||| | ||
ttttctgcattgctatggtggtgccacttgttcatcatccatcttataaaaaaagaacttgttgttcagcaa-aatgatgg-atactatttatttg---acat-agGTAAGGGAGATGCCAAATGTTTTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATCACGATATTGCAGT-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os10g38900.1 (Oryza sativa), 3'ss of exon 3
-ccactca-caatcatatatatatata-tgtctatcagtctacaacaatgatagttttaatacatagatgatgctaac-atactttgtgcatgtctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
|||| | || | | || ||| |||| |||| | | || | | | | || ||| | | ||||||| | | || |||||| |||||||| || ||||| || ||||| | ||||||||||||||||||||| || ||||| ||||| || || || || | | ||| | |||
gatactcttctattttcttgatgtattctgtcgttcagc--atgatgattaaactagagaatgatcaatgtcattgattatacttt-tactgctcactcacagGTGCGTGAGATGCCGAATGTATTAATTCTTCCTCGAAGTGCAGATTACAGTGAAGAAGTGTGGATTGAAATCAGAGAAAAGGCACTCGCAATATTGCAAT-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G460952_T01 (Zea mays), 3'ss of exon 1
--------------------------------------------------------------------------------ccact--cacaatcatatata----tatatatgtcta----tcagtctacaacaatgatagttttaataca---tagatgatgct-aacatact-----ttgtgcatgtctgcat-caggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
||||| |||||||| | | | | || | ||| ||| | | || | | | || || || | | || | | || ||| || | |||||| ||||||||| || || || || ||||| | |||||||| ||||||||||| || |||||||||||||| |||||||| ||| |||| ||||
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctgggggtggtgaagtaccctcagtgtcaccactaccacaatcacctgtgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G418294_T01 (Zea mays), 3'ss of exon 3
ccactcacaatcat-atatata-tatatgtctatcagtctacaacaatgatagttttaatacatagatgatgcta-acatactttgtgcatgtctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
| || | | || | | || | || | ||| | || | | || | | | ||||| | || | | |||| | |||||| |||||||| || ||||| || ||||| | ||||||||| ||||||||||| || |||||||| || || |||||||| || | ||| | ||
-actttgcacttgtgatgcttgctgtacttataatacgctaatagaaaagtcatgttt-caaacaaatgatttaatacttgttatgtgttcattgatcacagGTGCGTGAGATGCCAAATGTATTAATTCTTCCTCGAAGTGCAGACTACAGTGAAGAAGTGTGGATGGAGATCAGAGAGAAAGCAATCGCAATATTGCAGT-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G476107_T02 (Zea mays), 3'ss of exon 4
ccactcacaatcatatatatatatatgtctatcagtctacaacaatgatagttttaatacatagatgatgctaacatact--ttgtgcatgtctgcat-caggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
||| || ||| | | | || | | | || || | || |||| | ||||| || | | || ||| ||| | |||||| ||||||||| || || || || ||||| | |||||||| ||||| ||||| || |||||||||||||| |||||||| ||| |||| ||||
gtcctcgcag--ataaggacacgagttgctgttattttaacaccgttattgtttcattacattttgttcagcaaactggtgactgatcattgctgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGCGAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G394945_T01 (Zea mays), 3'ss of exon 2
--------------------------------------------------------------------------------ccact--cacaatcatatata----tatatatgtcta----tcagtctacaacaatgatagttttaataca---tagatgatgct-aacatact-----ttgtgcatgtctgcat-caggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
||||| |||||||| ||| | | || | ||| ||| | | || | | | || || || | | || | | || ||| || | |||||| ||||||||| || || || || ||||| | |||||||| |||||| |||| || |||||||||||||| |||||||| ||| |||| ||||
gtgagctgtctatgttgtatccttctggtacaggtgaggagggtgagagttctggtggtggtgaagtaccctcagtgtcaccactaccacaatcacctatgacccctcaaaattcaagaactcaacctatactttcaggatcttcatcagaaattacattttgttcagcaaagtggtgactgatcattgttgtgtacagGTGCGGGAGATGCCAAATGTTTTAATTCTTCCGCGGAGTGCAGACTACAGTAAAGAAGTGTGGATGGAAATAAGAGAGAAAGCAATAACTATGTTACAGT-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01510.1 (Arabidopsis thaliana), 3'ss of exon 3
------------ccactcacaatcatatat-atatatatgtctatcagtctacaacaatgatagttttaatacatagatgatgctaacatactttgtg-catgtctgcat--caggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
| | | | | | || | | || | | | | || | || | | | | || || ||| | || | | ||| | ||| ||||||||||| ||||| || || || || || || | ||||||||||||||||| || || |||||||| ||||||||||| ||||| ||||| | ||
gtatgactttcttttccagtgactaaacttcacatttgcgcctgcctattctcttgtttcatcatcttcttctgttgtttatcctg-catccattatatcttgttttcattgcagGTGAAGGAAATGCCAAATGTGTTAATTCTACCTCGCAGTGCAGATTACAGTGAGGAAGTATGGATGGAGATAAGGGAGAAGGCTATCTCTATCTTGCATT-
upper sequence: GLYMA18G47240.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv15s0046g02250.t01 (Vitis vinifera), 3'ss of exon 3
ccactcacaatcatatatatatata---tgtctatcagtctacaacaatgatagttttaatacatagatgatgctaacatactttgtgcatg--tctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
| ||| | ||| ||| | | | | | | |||||| | || ||| || |||| ||| | | |||| | ||| |||||| || || ||||| || |||||||| ||||| | ||||||||||| |||||||| ||||||||||| |||||||||||| |||| | |||| |||| |
---ggaaaaataaaatagccatacacaatattttttatgagttaacaattctgcattgtatatcaaggcgatgttaattagccccat-catgactttgcttcagGTAAAAGAAATGCCCAATGTATTGATTCTTCCACGCAGTGCAGATTATAGTGAAGAAGTTTGGATGGAGATAAGGGAGAAAACTATTTGTATATTACAGA-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|254332893|gb|GR850143.1|GR850143EST: TGGATGTGCTTTGGATGGGGCAGAAGGGCCTCAATGGATGGAAGCATGGG TGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTG
genomic: TGGATGTGCTTTGGATGGGGCAGAAGGGCCTCAATGGATGGAAGCATGGGtacggtaaat ... ctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatagttttaatacatagatgatgctaacatactttgtgcatgtctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
tgctaac putative branch site (score: 1)
ttttaatacatagat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ccactcacaatcatatatatatatatgtctatcagtctacaacaatgatagttttaatacatagatgatgctaacatactttgtgcatgtctgcatcaggTGAAGGAGATGCCTAACGTATTGATACTTCCCCAAAGTGCAGATTACAGTGAAGAGGTTTGGATGGAAATAAGGGAGAAAGCTATATCTATACTACAAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
-cactcac
- - - - - - - - - - - - - - - - - gtctaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgatgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcatgt