Sequence
atgc intronic sequence ATGC exonic sequencegtacatttgtgttttttgtttctattttaggttatttatatcagagtgcagtatttgatcatcttgtttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
Basic information
species | Glycine max |
transcript | GLYMA09G00280.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G00280.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os11g06750.1 (Oryza sativa), 3'ss of exon 5
-----------------------------------------gtacatttgtgttttttgtttc-tattttaggttatttatatcagagtgcagtatttgatcatcttgt-----ttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
| || | ||| || ||||| ||| || || | | | ||| | | || | || |||| || | ||||||||||||||| || ||||| |||||||| |||||||| || ||||| ||||||| || || | ||| | ||||| ||||||||||| || ||||||
gtaccaattcgtctaccagatattacaccagcactccatgattgcaaatctgtcttctgtttgatatgctattgcatctgtttgcgagcgaaac-ttaaacgatattgtgcttgctcttgcgctcagGACTGAGAAGGACATCACTCCCATGGGTGGCTTCCCTCACTACGGTGTTGTGAAGGGCGACTACCTCATGATCAAGGGTTGCTGTGTTGGCCCCAAGAAG
upper sequence: GLYMA09G00280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G324314_T05 (Zea mays), 3'ss of exon 5
---gtacatttgtgttttttgtttctattttaggttatttatatcagagtgcagtatttgatcatc--ttgtttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
|| | || | || | | || | | |||| | | ||| | ||| | | ||| | || | | ||||||||||||||| || ||||| |||||||| ||||| ||||||||| | ||||||| ||| || | ||| | ||||| |||||||| ||||| ||||||
gtactatttctgagcttgtactaacttgcacaatctgtttacctttgt-tgctcttgttggtaacgaattgctgcc-atttgcagGACTGAGAAGGACATCACTCCCATGGGTGGCTTCCCCCATTATGGTATCGTGAAGGGTGACTACCTGATGATCAAGGGCTGCTGTGTGGGACCAAAGAAG
upper sequence: GLYMA09G00280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G109677_T04 (Zea mays), 3'ss of exon 6
---gtacatttgtgttttttgtttctattt---taggttatttatatcagagtgcagtatttgat--catcttgtttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
|| | || | || |||| | || | | |||| | | ||| | ||| | | ||| | || | | ||||||||||||||| || ||||| |||||||| ||||| ||||||||| | ||||||| ||| || | ||| | ||||| |||||||| || || ||||||
gtactatttctgagcttcttgtactaacttgcacaatctgtttacctttgt-tgctcttgttggtaacgaattgctgcc-atttgcagGACTGAGAAGGACATCACTCCCATGGGTGGCTTCCCCCATTATGGTATCGTGAAGGGTGACTACCTGATGATCAAGGGCTGCTGTGTGGGTCCAAAGAAG
upper sequence: GLYMA09G00280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G801409_T04 (Zea mays), 3'ss of exon 4
---gtacatttgtgttttttgtttctattttaggttatttatatcagagtgcagtatttgatcat-cttgt---------ttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
|| | || | || |||| | | || || | ||| | | | | ||| || | |||| | | | | ||||||||||||||| || ||||| |||||||| ||||| ||||||||| | ||||||| ||| || | ||| | ||||| |||||||| || || ||||||
gtactatttctgagcttcttgtacatgtactaacttgcaca-atctgtttacctttgttgctcttgtttgtaacgaattgctgccatttgcagGACTGAGAAGGACATCACTCCCATGGGTGGCTTCCCCCATTATGGTATCGTGAAGGGTGACTACCTGATGATCAAGGGCTGCTGTGTGGGTCCAAAGAAG
upper sequence: GLYMA09G00280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G132968_T02 (Zea mays), 3'ss of exon 5
---gtacatttgtgttttttgtttctattt---taggttatttatatcagagtgcagtatttgatcat--cttgtttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
|| | || | || |||| | || | | |||| | | ||| | ||| | | ||| | || | | |||||| |||||||| || ||||| |||||||| ||||| || |||||| | ||||||| ||| || | ||| | |||||||||||||| || || ||||||
gtactatttctgagcttcttgtactaacttgcacaatctgtttacctttgt-tgctcttgttggttacggattgctgcc-atttgcagGACCGAGAAGGACATCACTCCCATGGGTGGCTTCCCCCACTATGGTATCGTGAAGGGTGACTACCTGATGATCAAGGGATGCTGTGTGGGTCCAAAGAAG
upper sequence: GLYMA09G00280.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G135727_T01 (Zea mays), 3'ss of exon 5
---gtacatttgtgttttttgtttctattt---taggttatttatatcagagtgcagtatttgatcat--cttgtttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
|| | || | || |||| | || | | |||| | | ||| | ||| | | ||| | || | | |||||| |||||||| || ||||| |||||||| ||||| || |||||| | ||||||| ||| || | ||| | |||||||||||||| || || ||||||
gtactatttctgagcttcttgtactaacttgcacaatctgtttacctttgt-tgctcttgttggttacgaattgctgcc-atttgcagGACCGAGAAGGACATCACTCCCATGGGTGGCTTCCCCCACTATGGTATCGTGAAGGGTGACTACCTGATGATCAAGGGATGCTGTGTGGGTCCAAAGAAGMapped 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|37997686|gb|CF809275.1|CF809275EST: GTTGCCAAGGCAGATCATGAGTCCCATTCAGCCATCACTGAATTTGACAG GACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGT
genomic: GTTGCCAAGGCAGATCATGAGTCCCATTCAGCCATCACTGAATTTGACAGgtacatttgt ... ctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGT
EST:
gi|58024229|gb|CX710970.1|CX710970EST: GTTGCCAAGGCAGATCATGAGTCCCATTCAGCCATCACTGAATTTGACAG GACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGT
genomic: GTTGCCAAGGCAGATCATGAGTCCCATTCAGCCATCACTGAATTTGACAGgtacatttgt ... ctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaggttatttatatcagagtgcagtatttgatcatcttgtttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
tcctaat putative branch site (score: 2)
tcatcttgtttcct CT-rich tract
ttatttatatcaga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatttgtgttttttgtttctattttaggttatttatatcagagtgcagtatttgatcatcttgtttcctaatgacagGACTGAGAAGGATATTACTCCTATGGGTGGGTTCCCTCATTATGGTGTGGTGAAGGATGATTATATTATGGTGAAGGGATGCTGTGTTGGACCGAAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG