Sequence
atgc intronic sequence ATGC exonic sequencegttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
Basic information
species | Glycine max |
transcript | GLYMA20G30430.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g47080.1 (Oryza sativa), 3'ss of exon 4
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
||| | | || | || | | ||| | |||| | | | |||| ||| |||||||||||||| || || ||||| ||||| || ||||||||| |||||| ||||||||||| || ||||| ||||| || |||||| ||||| |
------------------------------------------------------------------------------------gtaatagtcaacattcatttcactgaatattataaacactcttgtttcat-tctcattt-tctgaacttgc---agACAAGGATTGGGATGATATTAAGTTTGGTGTGGAGAATCAAGTTGACTACTATGCCGTTTCTTTTGTCAAAGATGCTCAAGTTGTGCATGAATTGAAGGA
upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G152686_T01 (Zea mays), 3'ss of exon 4
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggatta--aggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
| ||||| | | | || | | | | | | | | | | ||| || | | | |||||| ||||| ||||| ||||| || ||||| |||||||| ||||||| | |||||||||||| ||||| || ||||| ||||| || || ||||| ||| |
--------------------------------------------------------------------------------gtaatagtcggcaacttttttctgtctactggatctaatctatatatccttg---tttcatacacgtttcaaatg--tacagACAAGGACTGGGACGACATTAAGTTTGGTGTGGATAATCAAGTTGATTACTATGCTGTTTCCTTTGTGAAAGATGCTCAAGTTGTCCACGAACTCAAGGA
upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G52920.1 (Arabidopsis thaliana), 3'ss of exon 4
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgattt----gctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
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------------------------------gttcgaattttctgttt---accctctttttcactt---tttcttgttgctttggt-----tgaagtgttgcatatttaagtctgaaagatcttactctgatgcttattttttgtaattattttcttgccgcagAGAAGGACTGGGAGGATATTAAATTTGGAGTGGAGAACAAAGTTGACTTTTATGCAGTTTCCTTTGTCAAAGATGCTCAAGTTGTACACGAGTTGAAGAA
upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
| |||| || | | | || | || | | ||||||| | || | | | | ||| | |||| | || || | ||| | || || || | | | ||| ||| || | || ||||||| |||||||| || ||||| ||||||||||| ||||| || ||||| ||||| | || ||||| |||||||| || || || |||||||| |||
--------gtatgccatt-tttttgtgatcgaataaggcc---atatcga--tatttcttttgt-tgtcatatcttttatttag--actgtctgattta-gacactccgtcgcttgct--cttgtcacctacttttg-tttttctgtggaat--ctccagAGAAAGATTGGGAAGATATCAAGTTTGGAGTGGAAAACAAGGTGGACTTTTATGCCCTATCCTTTGTCAAGGATGCTCAGGTGGTGCATGAACTCAAGTC
upper sequence: GLYMA20G30430.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
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---------------------------------aatttcattagtgtgcaatcactatctctagagatctatagaaatttt-----atctgaacacggac-----tttggataccattgtgtttcc---------------ttctgtggagt--ctgcagAGAAGGATTGGGAAGACATTAAATTTGGAGTAGAAAATAAAGTTGATTTCTACGCGCTGTCATTTGTCAAGGACGCCCAGGTGGTGCATGAGCTCAAATCMapped 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|26048943|gb|CA785396.1|CA785396EST: GAGACATTTGAATGTTAGAGGAAAAAGTGCAACACTGCCTTCCATAACTG AGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCT
genomic: GAGACATTTGAATGTTAGAGGAAAAAGTGCAACACTGCCTTCCATAACTGgttagattct ... tttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
tgttgat putative branch site (score: 4)
atataatatttgtgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagattctggatcattattcctatacttgattgtttttttaattttaaaccatttcttctacatgcctctccatatgtttgggtactggcaaatgggtgaggattaaggttttgttggtttcccaaggacatataatatttgtgttgatttgctacagAGAAGGATTGGGATGACATCAAATTTGGAGTGGATAACAAAGTTGACTTCTATGCTGTTTCTTTTGTTAAGGATGCACAAGTAGTTCATGAACTGAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA