Sequence
atgc intronic sequence ATGC exonic sequencegttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTGTGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
Basic information
species | Glycine max |
transcript | GLYMA06G15520.2 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os01g73310.1 (Oryza sativa), 3'ss of exon 2
gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTGT-GACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
|| || | || || || | | || ||||| | |||| || | |||||| | | | || | | ||||| || ||||||| || ||||| || |||||||| ||||| || ||||||||||| ||||| || |||||||| ||||| |||||||| || |||||||
gtcaggaactt-catcttttaaaccatctat---catctccaagactccaactgcatttttac-caatttgaattccttaaaattt---tgcagGCTGGGTTTGCTGGAGATGATGCACCAAGGGCTGTTTTTCCTAGCATTGTTGGTCGTCCTCGCCACACTGGTGTCATGGTAGGGATGGGGCAGAAGGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g36290.2 (Oryza sativa), 3'ss of exon 2
gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTG-TGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
| ||| | | || | || || | ||| | || ||| || || | | || | | ||||||||| ||||||| ||| ||||| || ||||| || || || || ||||| || |||| ||||| || ||||| |||||||||||||| ||||||||||
-----------gtggttatcc-tgaacttagtcttttcagcaaagcggtatgttcctcatagcttaacggatcaccttcctaatgttta-acagGCAGGTTTTGCTGGTGATGATGCACCAAGGGCCGTCTTCCCTAGCATTGTAGGGAGACCACGTCACACCGGTGTCATGGTTGGGATGGGCCAAAAGGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g36650.1 (Oryza sativa), 3'ss of exon 2
----------gttagtactttgcagtttcttgtt-agtgtaattgc-atctatttagtcttggtttcattattgctcaatttat------ttaaatgatcat-ctgtgtacagGCAGGATTTGCTGT-GACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
|| | |||| ||| ||||| | |||| | | || | || | | | |||| | | || |||| || | | | | |||| || ||||||| || |||||||| | ||||| || || ||||||||||| || || || ||||| || ||||||||||||||||| ||||| ||||
gtaataaaaagtgatgacttggcatcgcattgttgaacaaaatttctacctgatggtaattattgttacaattgagaagctcatcaagtattaactgttttcatttttcatagGCTGGGTTTGCTGGAGATGATGCTCCCCGTGCTGTTTTCCCGAGTATTGTTGGCCGTCCGCGACATACAGGCGTTATGGTTGGGATGGGACAAAAAGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g01600.2 (Oryza sativa), 3'ss of exon 2
----gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTGTG-ACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
| | | ||| | ||| | ||||| || ||| | |||| | | |||| | ||| ||| || ||||| | |||| || || |||| | | ||||| || ||||| ||||| || ||||||||||| || ||||| || || ||||||||||| || ||||| || |||||||
gtctgattttctttttcttttttactcttacgtaatgtaatgtatgtcgtctcctgctgaatattac---attacattacatt-tcatc---atgtagGCTGGTTTCGCTGGGGATGATGCACCAAGGGCCGTGTTCCCTAGTATTGTTGGCCGTCCTCGCCACACCGGTGTTATGGTAGGAATGGGGCAGAAGGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G110378_T03 (Zea mays), 3'ss of exon 3
gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcat-tattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTG-TGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
|| || | || || | || | | | ||| || || ||| | | | |||| | | || || | | |||| || ||||||| |||||||| || |||||||| || || ||||||||||| || ||||| || |||||||||||||| |||||||| || |||||||
gtcagccccccctcccccctgacc--cccaacttgatttgtacaaccttatttccaagtatgccactaattatgtgtaccttctactct-tctagGCTGGTTTTGCTGGCGACGATGCACCAAGGGCTGTTTTCCCTAGTATTGTTGGCCGTCCTCGCCACACTGGTGTTATGGTAGGGATGGGACAGAAGGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G030169_T02 (Zea mays), 3'ss of exon 2
------gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttc--attattgctcaat-ttatttaaatgatcatctgtgtacagGCAGGATTTGCTGT-GACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
|| ||| ||| | || | | ||| | | || | | ||| ||| | ||||| ||| | | || || |||| || ||||||| || || ||||| | ||||| || || ||||| |||||||| || ||||| |||||||| |||||||||||||| || |||||||
gtaactgtagtcgcttggcatcatattctcta-atgattcctctttttccatacagcttttagattttcagtcaatgttaagcactttttccatctcttatagGCTGGCTTTGCTGGAGATGACGCTCCACGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGTCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G082484_T01 (Zea mays), 3'ss of exon 2
-------------------gtta-gtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttca-ttattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTGT-GACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
|| | | || ||||| ||| | || | || | ||| | | | ||||| | || ||| | | || ||||| | || |||| || ||||||| || |||||||| | ||||| || || ||||| |||||||| || || || |||||||| |||||||||||||| || |||||||
gtaattgtggccacttggcgtcatattctctgcagattcctttttttcaggcagcttttat--aatttaattttcagtcgatgttcattattttc---cccccatctct-tatagGCTGGCTTTGCTGGAGATGATGCTCCCCGTGCTGTTTTCCCAAGTATAGTTGGTCGTCCACGCCACACTGGTGTCATGGTTGGGATGGGACAGAAGGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: AT5G09810.1 (Arabidopsis thaliana), 3'ss of exon 2
----gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTG-TGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
||||| ||| | | || | | || | || | | | | | | || | | | | | || || | | | | |||||| || ||||||| ||| ||||| || || || ||||| || |||||||||||||| ||| | || |||||||| |||||||| |||||||| || ||||
gtgagttag-actgtttatttagatact-gtatggttctaaccttct--ttgttgtacatgtgtaagactactgatcatgatttttgtatattaacagGCTGGTTTTGCTGGTGATGATGCCCCGAGAGCAGTGTTCCCAAGTATTGTTGGTCGTCCTAGGCACACTGGTGTCATGGTTGGTATGGGTCAGAAAGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: AT1G49240.1 (Arabidopsis thaliana), 3'ss of exon 2
gttagtactttgcagtttcttgttagtgtaattgcatctattt--agtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTGT-GACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
|||||| | | || || || || || ||| | || |||| | | | || ||| ||||| ||||| |||| || |||||||| || || || || |||||| |||||||||||||| | ||| |||||| |||||||||||| ||| || ||||
---------------------gttagtctcttctttcttactttaaggattctcttaattttggcaagatttgat---acaagttcctttgtgcagGCTGGATTCGCTGGAGATGATGCTCCCAGAGCGGTTTTCCCCAGTGTTGTTGGTCGACCTAGACATCATGGTGTCATGGTTGGGATGAATCAGAAAGATG-
upper sequence: GLYMA06G15520.2 (Glycine max), 3'ss of exon 2
lower sequence: Vv04s0044g00580.t01 (Vitis vinifera), 3'ss of exon 3
-gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattattgctcaatttatttaaa---------tgatcatctgtgtacagGCAGGATTTGCTG-TGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
| | || || |||| || || | | | || | | | | | |||||||||| ||| | || | | | | ||||| |||||||| | ||| |||||||| ||||| |||||||| |||||||| ||||| || | || |||||||| |||||||||||||||||||| ||||
gtctgttgtttctttcttgcttgata-tgcagatttgttgtgttgtttgctgctcctcaaatgctcaatttgaataagctttccatgttatgctttatatgcagGCTGGATTTGCGGGTGATGATGCTCCCAGGGCAGTGTTTCCTAGTATTGTGGGTCGGCCAAGGCACACTGGTGTCATGGTTGGGATGGGTCAAAAAGATG-Mapped 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|6726695|gb|AW311040.1|AW311040EST: CTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAG GCAGGATTTGCTGGTGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTT
genomic: CTGAGGATATTCAACCCCTTGTTTGTGACAATGGAACTGGAATGGTGAAGgttagtactt ... ctgtgtacagGCAGGATTTGCT-GTGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttagtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTGTGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
tttcattattgctcaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtactttgcagtttcttgttagtgtaattgcatctatttagtcttggtttcattattgctcaatttatttaaatgatcatctgtgtacagGCAGGATTTGCTGTGACGATGCTCCTAGGGCTGTGTTTCCCAGTATTGTTGGTCGACCTCGTCATACTGGTGTTATGGTTGGGATGGGTCAAAAGGATGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG