Sequence
atgc intronic sequence ATGC exonic sequence...tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
Basic information
species | Glycine max |
transcript | GLYMA14G05430.2 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: GRMZM2G104920_T02 (Zea mays), 3'ss of exon 8
tttggcattttggttagtcaattcaa----attttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
|| || ||| | || ||| | || |||| | | | | | || | || | || | | | || |||| | || |||||| ||| | ||||| |||||||| ||||| ||||| | ||||| || ||||||||||| || |||| || ||||||||||||||||| || ||
-atgaatattaagttcatgaacacaacaacagatttttggtgtatgcattttcaagtaaggacaaaaaa--gaagaaataattacggctgttgtttatg-gcagGTGAAAGTGTGGTGCACAAATCAAGAAGCAAGTGTGATCAATATTGATATGAAAGCAAATATTTGCTCGGTTAAATATAATCCTGGATCAAGCTTCTACG
upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: AT2G32950.1 (Arabidopsis thaliana), 3'ss of exon 9
--tttggcattttggt--tagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagc-agGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
| | || || | |||| ||| | | || | ||||||| || || || | | || | ||| ||| ||||| | |||| ||| ||||||| || | |||||||| ||||| | ||||| || ||||||||||||||||| |||||||| || |||||||| || |||| || |
tttaagtcaattcactactagttaatcctcaaccatgcattattgcatctgttaaatcat-----gtctcatagattaaccaattgtgctgtgtgtttgatccagGTTAAAGTTTGGTGCACGAGGCAGGAAGCAAGTGTGATTAATATTGATATGAAAGCAAACATATGTTGTGTCAAGTACAATCCTGGCTCAAGCAACTACA
upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: Vv12s0059g01420.t01 (Vitis vinifera), 3'ss of exon 9
-----tttggcattttggt--tagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
|| || ||| | | | | || ||| ||| |||| || || || || || | | || |||||| | | | | ||||||||| ||||||| ||||| ||||| ||||| ||||| || || |||||||||||||| ||||| |||||||| ||||||||||||||| ||| |||||
agttcattataatcagggtactggggactccatattggtttgacatgctaaactaaccatagttt---gtatctgttatgaacttaatgtatgtaa----taaacagGTCAAAGTTTGGTGCACAAACCAGGAGGCTAGCGTTCTTAACATTGACATGAAAGCAAATATATGTTGTGTCAAGTATAATCCTGGATCTAGCATTTATA
upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S25_325V6.1 (Physcomitrella patens), 3'ss of exon 9
tttggcattttggttagtcaatt-caaattttcttggcatggtatctgttgtatgattgaaagtta---ttgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
|||||||| | ||| | | || | | | | || ||||| | | | | || || | | | ||| |||||| || ||||||| || |||||||| ||||||||| | | |||||||||||| || ||||| ||||| || || || |||||||| || |||| |||
-cccatgttttggttgcacgattacgggggaatataacagagactgtctcgt-tgattcttactcaagtcagccgttaaaagcagatggggggatttt--gcagGTTAAGCTTTGGTGCACTAATCAGGAGGCTAGTGTTTTTAGTATAGACATGAAGGCCAACATCTGCTGCGTTAAGTACAATCCTGGTTCAAGCAACCATA
upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: PP1S135_17V6.1 (Physcomitrella patens), 3'ss of exon 9
---------------------------------------tttg--gcattttggttagtcaa-----ttcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctct-tgtctttga--gcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
||| || || ||| |||| |||||| | | ||| | | | || || | | | | | | ||||| | | ||| || |||||| || || ||||| || | || || | || || |||||||||||||||| ||||| || |||||||| || |||||||||||||| ||| |||
gtaacctgttgaaatctggtgaacttaatcactcttgtacttgatgcggttctgtttttcaagctttttcaaactcaggttatttggagttttccgcatcatgtttaatatgcggttgatccgaaatgtttttatgttactgtttgcagGTGAAGATATGGTGCACGAGGCAAGAGTCAAGCGTGATAAATATAGACATGAAGGCAAATATTTGCTGTGTGAAGTATAATCCTGGATCAAGCAGCTATG
upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ20512 (Selaginella moellendorffii), 3'ss of exon 9
tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttga---gcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
||| | ||| | ||| | ||| ||| | | || ||||| |||||||| | ||||| || | ||||| | ||||| || || || |||||||| |||||||| |||||||||||||| ||||| |||||| |||||| |
-----------------------------------------------gtgttttattattacttacacacccgaattccctgtttgt-gtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTG
upper sequence: GLYMA14G05430.1 (Glycine max), 3'ss of exon 9
lower sequence: EFJ28584 (Selaginella moellendorffii), 3'ss of exon 9
tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttga---gcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
| ||| | ||| | ||| | ||| | ||| | | || ||||| |||||||| | ||||| || | ||||| | ||||| || || || |||||||| |||||||| |||||||||||||| ||||| |||||| |||||| |
--------------------------------------------gtagtgttttattattacttacacacccgaattcactgtttgt-gtttttgacgcacagGTCAAGCTGTGGTGCACCAGGCAGGAGACAAGTGTCCTGAACATTGACATGAAGGCAAACATTTGCTGTGTCAAATACAATCCCGGATCTAGCAATTTTGMapped 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|105633923|gb|DW247286.1|DW247286EST: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG GTCAAAATTTGGTGT
genomic: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtacttgaaa ... ctttgagcagGTCAAAATTTGGTGT
EST:
gi|193629154|gb|FK578102.1|FK578102EST: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG GTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATA
genomic: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtacttgaaa ... ctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATA
EST:
gi|9564187|gb|BE473696.1|BE473696EST: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAG GTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATG
genomic: TTTCAAGAACAGACCCCTCTATGCTTGTATCTGGTAGCGATGACTGTAAGgtacttgaaa ... ctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
tattgat putative branch site (score: 3)
tgtctcttgtcttt putative PPT
ttattgatgtaaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttggcattttggttagtcaattcaaattttcttggcatggtatctgttgtatgattgaaagttattgatgtaaatgtaatgtctcttgtctttgagcagGTCAAAATTTGGTGTACAAATCAGGAAGCTAGTGTTCTAAATATAGACATGAAAGCAAACATATGCTGTGTCAAATATAATCCTGGATCTGGCAATTATA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- -ggcattt
- - - - - - - - - caattca
- - - - - - - - - - - - - - - - - -gcatggt
- - - - - - - - - - - - - - - - - - - - - - - - tgtatga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgatgta