Sequence
atgc intronic sequence ATGC exonic sequencegtgagtttctgcatctgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
Basic information
species | Glycine max |
transcript | GLYMA11G01820.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA11G01820.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g71320.1 (Oryza sativa), 3'ss of exon 6
---gtgagttt--ctgcatctgatgactcctgttgcttgatttgtcat---gactaaa-attttggag-atttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
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gtagcaacctgggtaaaattcaattattctggtatcttgtgttgtggtttagactgaacactttgtactaccatgattcagGGCTTTGAGAAAATGATATCAGGAATGTATCTTGGGGAAATTGCAAGATTGGTATTTCATAGAATGGCCCAGGAATCAGATGTTTTTGGTGATGCTGCTG
upper sequence: GLYMA11G01820.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G50460.1 (Arabidopsis thaliana), 3'ss of exon 6
--------------------gtgagtttctgcatctgatg----actcctgttgcttgatttgtcatgactaaaat--tttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
|| |||| | || || | | | | || | | | | || || ||||| | || |||| |||||||| |||||||||||||||||||| |||||||| || | ||||| |||||| |||||| ||| || ||||| |||||||| || || |
gtaatctttgccatacttccctgtttttccg-atttggtattgcgttattagtttttaaccaattaacatcaacatcatttggggtttcttacatagGGATTTGAGAAGATGATATCAGGAATGTATCTGGGTGACATTGTTCGTAGAGTAATTCTCCGCATGTCAGAAGATTCTGATATCTTTGGACCCATCTCGC
upper sequence: GLYMA11G01820.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv06s0061g00040.t01 (Vitis vinifera), 3'ss of exon 6
------gtgagtttctgcatctgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
| | || || || | || | | || | | | || | || |||||| | ||| | | |||||||||||||||||||||||||| ||||| | |||||||| ||||| ||||| ||||||| |||||| ||||| || || |||||||| |||||
gtacagttcaattacttgcccttgtctcttc-gatgttccagtgaaca-aatcaagattttgaggcttttgtttcagGGTTTTGAGAAAATGATATCAGGGATGTACTTGGGTGACATTGTGAGGAGAGTTATTCTCAGAATGTCACAGGAGTCAGACATTTTTGGACCTGTTTCTT
upper sequence: GLYMA11G01820.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14634 (Selaginella moellendorffii), 3'ss of exon 6
gtgagtttctgcatctgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtg-cagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGG-ACCAATTTCTC
| ||| | | ||||||| | || | | || | || || ||| |||||||| || | || ||||||||||| |||||||| ||||| || |||||||||||| | | || | | ||||| || |
------------gtgagatacttgcaattgcttg------tacagctga-----cgcagctgtgcctggtagGCGTTTGAGAAGCTGTTTTCGGGAATGTATCTGGGTGACATTGTGAGGAGGGTCATTCTCAAGCTTGCGCAGGATGCCTGCCTATTTGGCGGCAGCATAC-
upper sequence: GLYMA11G01820.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ10895 (Selaginella moellendorffii), 3'ss of exon 6
gtgagtttctgcatctgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
|| || || ||||| | | | | | | | | | |||| || || || |||||||||||||| |||||||| || |||||||| ||||| ||||| | || || | || ||| | |||||| || |
gtaagcttgaa-----aatgaccacaaaaacaattcctaccctaccctacctgt-----gtttgactgtagATATTCGAGAAAATGATATCTGGAATGTACCTGGGTGACATTGTGAGGAGAGTGTTGTGGAAACTGGCTGCCGAAGCGGCATTCTTTGGAGGAAAGGTACMapped 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|254322469|gb|GR837883.1|GR837883EST: CGTCGTATGACATTGACTTGGATGCTGAGAGCCCAAATCCAAATGATCAG GGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGA
genomic: CGTCGTATGACATTGACTTGGATGCTGAGAGCCCAAATCCAAATGATCAGgtgagtttct ... ttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGA
EST:
gi|7795161|gb|AW780558.1|AW780558EST: CGTCGTATGACATTGACTTGGATGCTGAGAGCCCAAATCCAAATGATCAG GGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGA
genomic: CGTCGTATGACATTGACTTGGATGCTGAGAGCCCAAATCCAAATGATCAGgtgagtttct ... ttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
gactaaa putative branch site (score: 2)
atgactaaaatttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtttctgcatctgatgactcctgttgcttgatttgtcatgactaaaattttggagatttgggtgcagGGTTTTGAGAAAATGATATCAGGAATGTATCTTGGTGACATCGTGAGAAGAGTCATTCTCAAGATGTCATTAGAGTCGGATATGTTTGGACCAATTTCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG