Sequence
atgc intronic sequence ATGC exonic sequencegtatattgctcttcaatgtcttttaagtatgaaaatacttgttgatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
Basic information
species | Glycine max |
transcript | GLYMA08G04890.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G109383_T02 (Zea mays), 3'ss of exon 12
gtatattgctcttcaatgtcttttaagtatgaaaatacttgtt--gatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
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---------------------gtaaaatattaaaatcttggtttgcaagatttttgaatgtcatataaatctgacataaaaaaaccatgtttcagGTGCCTACTGGATGGAAGTTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G023289_T03 (Zea mays), 3'ss of exon 12
gtatattgctcttcaatgtcttttaagtatgaaaatacttgtt-gatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
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---------------------gtaaagtattaagaccttggtttgcaagattttgaatgctagataaatctaac--ataaaaaacatgtttcagGTGCCTACTGGGTGGAAATTTTTTGGGAATTTGATGGATGCTGGAATGTGCTCAATCTGTGGTGAAGAAAGCTTTGGCACTG
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
lower sequence: AT1G23190.1 (Arabidopsis thaliana), 3'ss of exon 12
--gtatattgctcttcaatgtcttttaagtatgaaaatacttgttgatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
|| | | | ||| ||| | || | | | | |||| || || | |||| ||| | | ||||| || || || |||||||| ||||||||| | ||||||||||| | ||||| || ||||| |||||||||||||| ||||
gtacatgtcaccgtgcaacttctatccagcttcttttctcctaactacataattta---atttcatatctctattaaatcac------atatcagGTTCCAACAGGCTGGAAGTTTTTTGGTAATCTGATGGATGCTGGGATGTGTTCTGTTTGTGGAGAAGAAAGTTTTGGAACTG
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 3'ss of exon 13
gtatattgctcttcaatgtcttttaagtatgaaaatac-ttgttgatggctttta-gacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
||| |||| | | ||| | | | | | | | || || | ||| || || ||| | | ||||| ||||||||| || || ||||| || |||||||| |||||||||||||||||||||||| | |||||||||||||||||||| ||||
--gtatcctgtttcacattttattagattcttttgtgcgtcatataccacagctatgagaggca--tacatttgttattgactgttcaatgccagGTCCCAACTGGCTGGAAATTTTTTGGTAACTTAATGGATGCTGGATTATGTTCAATTTGTGGTGAAGAAAGTTTTGGAACTG
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ09195 (Selaginella moellendorffii), 3'ss of exon 11
gtatattgctcttcaatgtcttttaagtatgaaaatacttgttgatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
|| || |||||| | ||||| ||| | || | || ||| |||||||| || || |||||||| ||||| || || ||||||||||| | ||||| ||||||||||||||||||| || || |
-----------------------gtgataggattgctcttgttc-ttgctttcctacacacgcgtacat-gttgcgttg-----------cagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCG
upper sequence: GLYMA08G04890.1 (Glycine max), 3'ss of exon 12
lower sequence: EFJ05270 (Selaginella moellendorffii), 3'ss of exon 11
gtatattgctcttcaatgtcttttaagtatgaaaatacttgttgatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
|| || |||||| | ||||| ||| | || | || ||| |||||||| || || |||||||| ||||| || || ||||||||||| | ||||| ||||||||||||||||||| || || |
-----------------------gtgataggatttctcttgttc-ttgctttcctacacacgcgtacat-gttgcgttg-----------cagGTCCCTACTGGATGGAAGTTTTTTGGAAACTTGATGGATGCTGGCATGTGTTCCATCTGTGGTGAAGAAAGTTTCGGAACCGMapped 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|58015854|gb|CX702596.1|CX702596EST: CCAAACATCTGAATTTG-AATTTTTTGAG GTCCCCACGGNTTGGAAGTTCTTTGGTAA-TTAATGGATGCTGGATTATGT
genomic: CCAAACATCTGAATTTGAAATTTTTTGAGgtatattgct ... tcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttgatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
atttaat putative branch site (score: 4)
ttttagacatgcaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatattgctcttcaatgtcttttaagtatgaaaatacttgttgatggcttttagacatgcaattattttatttaattgttattcaaaaccagGTCCCCACGGGTTGGAAGTTCTTTGGTAATTTAATGGATGCTGGATTATGTTCAGTCTGTGGTGAAGAAAGTTTTGGGACTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA