Sequence
atgc intronic sequence ATGC exonic sequencegtatagttacttgttcattttatggtaattaaggcttgattttcacttttaaagttcttattgcaataatattttcttcaattcctgataataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
Basic information
species | Glycine max |
transcript | GLYMA20G38320.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G38320.2 (Glycine max), 3'ss of exon 8
lower sequence: LOC_Os01g14950.1 (Oryza sativa), 3'ss of exon 8
gtatagttacttgttcattttatggtaattaaggcttgattttcacttttaaagttcttattgcaataatattttcttcaattcctgataataa-----acagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
| | || | | | | ||| || | | || || | || | | || | | || ||| ||||| | | | | ||||||| || | ||| | |||| |||| |||| |||||||| |||| || ||||| ||||||||||| |||||||| ||||| |||||||||||||
gcaatctttcgtccttaacctataatagcctatagctatagatcttgttgattgtgcatgttc---tgaaatgttcaacaatttgctgcattgactaccatagGCTGTCATAAATGCTGGCATTATTGGTCCTCTGGTGAATCTGCTCCAAACGGCAGAGTTCGATATCAAGAAGGAAGCTGCATGGGCCATCTCAAATGCTA
upper sequence: GLYMA20G38320.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G088231_T01 (Zea mays), 3'ss of exon 8
gtatagttacttgttcattttatggtaattaaggcttgatt--ttcac---ttttaaagttcttattgcaataatattttcttcaattcctgataataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
| ||| | || || || | | | | |||| || |||| || ||| | ||| | | || | ||| | ||| ||||||| || || | | || ||||||||| | | |||||||||| || ||||||||||||||||| || ||||||||||| |||||||||||||
--actattaataatttatattttctcactacatgcttctttgcttcatgtgttcaaaaaatgttagtaattgattactcgctttgctgtact-caatttttagGCTGTCATAAGTGCCGGTATCATCGCTCCTTTGTTGCAACTGCTTCAAACAGCAGAGTTTGATATCAAGAAGGAGGCTGCTTGGGCCATCTCAAATGCTA
upper sequence: GLYMA20G38320.2 (Glycine max), 3'ss of exon 8
lower sequence: GRMZM2G091119_T02 (Zea mays), 3'ss of exon 7
gtatagttacttgtt-cattttatggtaattaag--gcttgattttcact--tttaaagttcttattgcaataatattttcttcaat-tcctgataataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
|| ||| || | || | | | | | ||| |||| | || || | ||| | | || | ||| || | |||| || ||||||| || ||| | | || ||||||||| | | ||||||||| || ||||||||||||||||| || ||||||||||| |||||||| ||||
--atttttatttttcacagatgacccatgtcatgcttctttgccttcatttgttcgaaaatgttagtcattgattactcactttgatatgctga--atttttagGCTGTCATAAGTGCTGGTATTATCGCTCCTTTGTTGCAACTGCTTCAAGGAGCAGAGTTTGATATCAAGAAGGAGGCTGCTTGGGCCATCTCAAACGCTA
upper sequence: GLYMA20G38320.2 (Glycine max), 3'ss of exon 8
lower sequence: Vv14s0060g01510.t01 (Vitis vinifera), 3'ss of exon 8
gtatagttacttgttcattttatggtaat-taaggcttgattttcac---ttttaaagttcttattgcaataatattttcttcaattcctgataataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
||| ||| || ||||| ||| | | | || ||||||| | || || || | || || | ||| | ||| | | | |||||||| |||||||| || |||||| ||| | || ||||||||||||||||||||||||||||||||||||| ||||||||||| |||||||||||||
-catatagactgatttattttgtggatgtatcatatttcattttcatacatgctagggtactgaatgatgta-tgtttgtatgtattttcaaaattttgcagGCTGTAATTGAGGCAAACATAATTGGTCCCCTTGTTCATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAGGCTGCTTGGGCAATCTCAAATGCTA
upper sequence: GLYMA20G38320.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S165_54V6.1 (Physcomitrella patens), 3'ss of exon 8
gtatagttacttgttcattttatggtaatt-------aaggcttgattttcac-----ttttaaagttcttattgcaataatatttt-cttcaattcct--gataataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
||| | || || |||||| | || || || || || || | | ||| ||| | || | ||| ||||| | | || || ||| | ||||||| ||||| || || | ||| | |||||||| ||| ||| | || || ||||| |||||||| ||||||||||||||||| |||||||| |
gtaaaaatattt-ttcattgtgtgatacttgttcaaaaatatttatttcttgcatgcacttttgagtgatggttcgactaacattttacattgtttgcttcgatgctctgtagGCTGTTATTGATGCCAACATCATTCCACCTTTGGTATCTCTTCTTGCCACCGCAGAATTTGACATCAAGAAGGAAGCTGCTTGGGCTATTTCAAATGCCA
upper sequence: GLYMA20G38320.2 (Glycine max), 3'ss of exon 8
lower sequence: PP1S230_50V6.1 (Physcomitrella patens), 3'ss of exon 7
--------gtatagt-tacttgttcattttatggtaattaaggcttgattttcacttttaaagttctt-attgca----ataatattttcttcaattcctg-ataataa-------------------acagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
| | | | ||| |||| | || | ||| | ||| |||| || | | || | |||| || | | || |||| || | |||| |||||| |||||||| || || | ||| | || | || | |||| | |||||||||||| |||||||||||||| ||||||||||| || ||||| |
gtattaatttccactctccttattcaatccctgttgattggagattgcttttattttccactcctgttcactgcactgtgtagtcatacttttaattgatgtactataatcgttttcggttgtctactacagGCCGTGATTGACGCGAACATTATTCCACCGCTTGTATCTTTGCTCGCCACTGCTGAGTTTGACATCAAGAAAGAAGCAGCTTGGGCTATTTCGAATGCCAMapped 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|254331218|gb|GR845797.1|GR845797EST: CTTGTTGGACCATATCCAATATCACAGCTGGTAATAAGCAGCAGATTCAG GCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAAT
genomic: CTTGTTGGACCATATCCAATATCACAGCTGGTAATAAGCAGCAGATTCAGgtatagttac ... taataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAAT
EST:
gi|22525688|gb|BU084499.1|BU084499EST: CTTGTTGGACCATATCCAATATCACAGCTGGTAATAAGCAGCAGATTCAG GCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAAT
genomic: CTTGTTGGACCATATCCAATATCACAGCTGGTAATAAGCAGCAGATTCAGgtatagttac ... taataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cacttttaaagttcttattgcaataatattttcttcaattcctgataataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
tcctgat putative branch site (score: 3)
ttaaagttcttattgc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatagttacttgttcattttatggtaattaaggcttgattttcacttttaaagttcttattgcaataatattttcttcaattcctgataataaacagGCTGTGATTGAGGCTAATCTAATTGCTCCTTTGGTCAATCTGCTTCAAAATGCTGAGTTTGATATCAAGAAAGAAGCTGCTTGGGCTATCTCAAATGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT