Sequence
atgc intronic sequence ATGC exonic sequencegtatatatgtacattacagataattgaaaaatgctgccatccttttaactaatgcttattgtaaacaatattctagaactaggatatataagattgttttttctatggatcttgtgctgcagGAAATTGTGAACCTACTGCTCTGTGGGGAGGCTGTTCCTAATGTGTTTGATGGAAGGATGGATTTAGGAGGAGGAATGTTTGTGAAAGGTATATCCGGAT
Basic information
species | Glycine max |
transcript | GLYMA20G30610.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G30610.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G042782_T01 (Zea mays), 3'ss of exon 2
gtatatatgtacattacagataattgaaaaatgctgccatccttttaactaatgcttattgtaaacaatattc-tagaacta-ggatatataagattgttttttctatggatcttgtgctgcagGAAATTGTGAACCTACTGCTCTGTGGGGAGGCTGTTCCTAATGTGTTTGATGGAAGGATGGATTTAGGAGGAGGAATGTTTGTGAAAGGTATATCCGGAT-
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-------------------attatagtaacattttattctatatttattttgcacagctt-tgatcattattaatacaattgtggtcaaataagatatagtgacttaattgtcttat----cagGAAATTGTGAATTTATTGCTCTGTGGAGAGGCTGTTCCAAATGTATTTGATGGCAAGATGGACCTTGGTGGTGGCATGTCCTTGAAGGGCATA-CCAAACA
upper sequence: GLYMA20G30610.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G129781_T01 (Zea mays), 3'ss of exon 6
gtatatatgtacattacagataattgaaaaatgctgccatccttttaactaatgcttattgtaaacaatattc-tagaacta-ggatatataagattgttttttctatggatcttgtgctgcagGAAATTGTGAACCTACTGCTCTGTGGGGAGGCTGTTCCTAATGTGTTTGATGGAAGGATGGATTTAGGAGGAGGAATGTTTGTGAAAGGTATATCCGGAT-
|| || | || || | | |||| | | || | | || |||| || || | || | ||||||| | || |||| | |||||||||||||| || | |||||||| ||||||||||| ||||| |||||||| | |||||| | || || || |||| |||| || ||| || |
-------------------attatagtaacattttattctatatttattttgcacagctt-tcatcattattaatacaattgtggtcaaataagatatagtgacttaattgtcttat----cagGAAATTGTGAATTTATTACTCTGTGGAGAGGCTGTTCCAAATGTATTTGATGGCAAGATGGACCTTGGTGGTGGCATGTCCTTGAAGGGCATA-CCAAACA
upper sequence: GLYMA20G30610.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G43690.1 (Arabidopsis thaliana), 3'ss of exon 6
gtatatatgtacattacagataattgaaaaatgctgccatcctt-ttaactaatgcttattgtaaacaatattctagaactaggatatataagattgttttttctatggatcttgtgctgc-agGAAATTGTGAACCTACTGCTCTGTGGGGAGGCTGTTCCTAATGTGTTTGATGGAAGGATGGATTTAGGAGGAGGAATGTTTGTGAAAGGTATATCCGGAT
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------------gtaataga--acaaacacatttcagaatctagactggttaattgtttctcctacttctatcctgtgttttgagttctactgatt--tttctctatgcctctttttttattagGAAATTGTAAACCTGCTGCTGTGTGGAGAAGCGGTTCCTAATGTATTTGATGGACGGATGGATCTTGGAGGCGGCATGTTTCTGAAAGGCATATCTAAGA
upper sequence: GLYMA20G30610.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv18s0072g00780.t01 (Vitis vinifera), 3'ss of exon 6
gtatatatgtacattacagataattgaaaaatgctgccatcc----ttttaactaatgcttattgtaaac----------aatattc----tagaactaggatatataagatt---gttttttctatggatcttgtgctgcagGAAATTGTGAACCTACTGCTCTGTGGGGAGGCTGTTCCTAATGTGTTTGATGGAAGGATGGATTTAGGAGGAGGAATGTTTGTGAAAGGTATATCCGGAT
||||| || ||||||| | || | | | | | || | | || || | | | |||| | || | | | ||||||| | | || | | || || || || ||||||||||| ||| ||||||| || ||| ||||||| |||||||||||||||||||||||||||||||| || || |||| | |||| || |||||| ||
gtatacatactacctacagatcactgttcacttccctcttttggtgcttcattgattgtttgctatggatgcgctgccttaatagttgcattatgattggattatataaaaattatgtcctacccttgaattttatggaacagGAAATTGTAAACTTACTGCTATGCGGGCAGGCTGTCCCTAATGTGTTTGATGGAAGGATGGATTTAGGTGGGGGCATGTCTTTGAAGGGAATATCCACAT
upper sequence: GLYMA20G30610.1 (Glycine max), 3'ss of exon 6
lower sequence: EFJ04910 (Selaginella moellendorffii), 3'ss of exon 6
gtatatatgtacattacagataattgaaaaatgctgccatccttttaactaatgcttattgtaaacaatattctagaactaggatatataagattgttttttctatggatcttgtgctgcagGAAATTGTGAACCTACTGCTCTGTGGGGAGGCTGTTCCTAATGTGTTTGATGGAAGGATGGATTTAGGAGGAGGAATGTTTGTGAAAGGTATATCCGGAT-
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----------gctactctgttcttt------tcttgtctgcccttgctcttaagctgttaggaaaccatctcct-----tttttctcgtgggcctgacctctctttgc-tcgtgtcttgcagGAGATTGTGAACCTGCTGCTCTGCGGCCAGGCTGTTGCAAATGTGTTTGACGGGAACTACGACCTTGGGGGTGGCATGAGCCTCAAGGGAAT-CCCGTCCA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atattctagaactaggatatataagattgttttttctatggatcttgtgctgcagGAAATTGTGAACCTACTGCTCTGTGGGGAGGCTGTTCCTAATGTGTTTGATGGAAGGATGGATTTAGGAGGAGGAATGTTTGTGAAAGGTATATCCGGAT
atatataagattgttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatatatgtacattacagataattgaaaaatgctgccatccttttaactaatgcttattgtaaacaatattctagaactaggatatataagattgttttttctatggatcttgtgctgcagGAAATTGTGAACCTACTGCTCTGTGGGGAGGCTGTTCCTAATGTGTTTGATGGAAGGATGGATTTAGGAGGAGGAATGTTTGTGAAAGGTATATCCGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA