Sequence
atgc intronic sequence ATGC exonic sequence...ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatgaaacatttgtttttgttcttgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
Basic information
species | Glycine max |
transcript | GLYMA18G49580.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os08g33830.1 (Oryza sativa), 3'ss of exon 8
---ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatgaaacatttgtttttgttcttgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
| | | || ||| | | | ||| | | | | ||| | || | | || || |||| ||||||| |||| ||||||| ||| ||||| | ||||| | || ||||| |||||||||||||| || || |||||||||||||| ||||||||||||||||||||
atctattttacttcagcttttcaatgatctaatcatgcattgca-ataccattttagtttattggagttatcttataattgaaaa-aactgttttattgcagACATCACAACGGCAGCAGTTGCTAAACAAGCTTTGGAAGGGCACTGCATATATGATGGAGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA-
upper sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os03g25980.1 (Oryza sativa), 3'ss of exon 8
ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatg----aaacatttgtttttgttcttgatcatgtgtaa--acatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
|| ||| || | | | | |||| || || || ||| ||| ||| ||||| | | ||||| | ||||| | | || || |||| ||| | ||||| | || ||||||||||| || ||||||||||| |||||||| || || ||||| ||||||||||||||
----ctttacatcgtaacaaacatg-tgcttgttctgtttatgatttcatgtgctttaaattcagacattttttcatgatctgacttcattacattaccattcagATGTAACTACAGCTTCAGTTGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGTGGCTACTGTAAGCTCCACCTGTCATATTCTCGTCATACTGA-
upper sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G178169_T01 (Zea mays), 3'ss of exon 8
ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatga--aacatt--tgtttttgttcttgatcatgtg--ta--aacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
| | | || ||| | ||| | || | || | || | | || ||| || | | | |||| || || || || ||||| |||||| | ||| ||| | | ||||| | ||||| | ||||| || ||||||||||||||||| || |||||||||||||| ||||||||||||||||||||
-------agtggtattgctaattctgtttcccccttggccatggtactatagcattaatattgatggacaaatacatagtcatctgactagcaaaatctttttttagATATAACAACTGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA-
upper sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G082174_T03 (Zea mays), 3'ss of exon 9
ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttc-ttgatgaaacatttgtttttgttcttgatcatgtg--taa--acatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
||||| | || | | | | || | | || | | || || || || | | | |||| || ||| | || ||||| |||||| | || ||| | | ||||| | ||||| | ||||| || ||||||||||||||||| || |||||||||||||| ||||||||||||||||||||
ggaattg--ctagtt--ctgtttcccccttagccatggaaatatatcattaatatttgatgtacaaatacataggttcatctgactaacaaaatctttttttagATATAACTACCGCAGCCGTTGCTAAACAAGCTTTGGAGGGACACTGCATATATGATGGTGGTTACTGTAAGCTTCATCTGTCATACTCTCGTCATACTGA-
upper sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM5G883601_T01 (Zea mays), 3'ss of exon 8
-----ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatgaaacatttgtttttgttcttgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
| ||| | ||| |||| | ||| || | ||||| | || ||| | | | |||| | || | | || | |||| | | || || | | || | ||||| | || ||||||||||| || ||||| ||||| ||||||||||| || |||||||| |||||||||||
actttctcactaaac-atgcagctgattatttcattttcccatgtgcttttctatagaaattattcatctgaatc--tgattaagtcttt-ctttacactttagATGTAAATACTGCCGCTGTAGCGAAGGAAGCATTGGAAGGGCATTGCATCTACGATGGCGGCTACTGTAAGCTTCACCTGTCATACTCCCGTCATACTGA-
upper sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0108g01030.t01 (Vitis vinifera), 3'ss of exon 8
------ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatgaaacatttgtttttgttcttgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
| | || || | | || | | | | | || | || || ||||| ||| ||| ||| ||||| ||| ||| ||| ||| ||| | ||||||||||||||| || ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
tcaattttatttctaccaccatagggaatggttggcaattttatttatatctcatccctccactgctgggcagacaaatgatctgttgt-----tttctttccagATGTCACAACTGCAGCAGTTGCCAAAGAAGCTCTAGAGGGACACTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGA-
upper sequence: GLYMA18G49580.1 (Glycine max), 3'ss of exon 8
lower sequence: PP1S326_1V6.1 (Physcomitrella patens), 3'ss of exon 8
ggaatggaactgggtagcagatt-tactagccctcctgtgcgtg-tttcttgatgaaacatttgtttttgttct-tgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
| || | | | ||||| | || | | | | | | || || | | | | | || | || || || | ||||||| || ||| | || | |||||| || || || || ||||| || ||||| || | || ||||||||||||||||||||||| ||||||||
--agtgtcaagagctctgagattgtgctggatggtttattagcggccttttaatatggttctagctagcatccaacgagtttttgctttttttcttctacagATATTCCTACTGCAGTTGGAGCAAAAGAAGCACTCGAAGGTCACTGCATTTACGATGGCGGTTTCTGCAAGCTTCATCTATCATACTCTCGGCATACTGA-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|23057524|gb|BU578198.1|BU578198EST: GCTATATTTGAAAAGAACGGTCAAACTCAGGCACTGATTCAGTACCCTGA TATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATA
genomic: GCTATATTTGAAAAGAACGGTCAAACTCAGGCACTGATTCAGTACCCTGGtattaatcat ... tttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATA
EST:
gi|9565982|gb|BE475491.1|BE475491EST: GCTATATTTGAAAAGAACGGTCAAGCTCATGCACTGATTCAGTACCCTGA TATCATAACTGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATCGCATATA
genomic: GCTATATTTGAAAAGAACGGTCAAACTCAGGCACTGATTCAGTACCCTGGtattaatcat ... tttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttgatgaaacatttgtttttgttcttgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
tcttgat putative branch site (score: 4)
cattttttt putative PPT
tgtaaacattttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggaatggaactgggtagcagatttactagccctcctgtgcgtgtttcttgatgaaacatttgtttttgttcttgatcatgtgtaaacatttttttgcagaTATCATAACGGCATCAGCTGCTAGAGAAGCTCTAGAGGGGCATTGCATATATGATGGTGGCTATTGTAAGCTTCATCTATCATACTCTCGTCATACTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - gccctcc
- - - - - - - - - - - - - - - - - - -tgcgtgt
- - - - - - - - - - - - - - - - - - - - - - - cttgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tcatgtg