Sequence
atgc intronic sequence ATGC exonic sequence...tatatgattctgcaggctcagcactcagtttcaagcctgaattttttatgaaagggattttaacgataacctatgtacacttgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
Basic information
species | Glycine max |
transcript | GLYMA18G52270.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g06499.2 (Oryza sativa), 3'ss of exon 4
tatatgattctgcaggctcagcactcagtttcaagcctgaattttttatgaaagg---gattttaacgataacc-tatgtacact--tgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
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------aaactatcttctaagttttagggggcaaaaccaaaatcatttagatatgcttaatttttactatagttatgttgccaatgatatgtgttcttatttacagGCTCGGTTGGCTTATTCGATTTATTAGCCATTCTGTCATATCTGGCTTCACTACTGCTTCAGCTATTGTAATTGGTCTGTCACAGATCAAGTATTTCTTG
upper sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G068212_T01 (Zea mays), 3'ss of exon 3
------tatatgatt---ctgcaggctcagcactcagtttcaagcctgaattttttatgaaagggattttaacgataacctatgtacacttgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
| | ||| | || | || || | | | || | || | || || | |||| || | ||||| || | || | | ||||||||| ||||| |||||||||||||||||||| || || ||||| || || || |||||||| ||||| ||||||||||| || || || |||||
aatattttcttaatttgatagtagaacaaatacacaatcttg-gtatgcttgttctctgtgagaatgtgtaaccatttcatatgt---tttattttgta-----tacagGCTTGGTTGGCTCATTCGTTTCATTAGCCATTCTGTAATATCTGGGTTCACTACAGCTTCAGCCATTGTTATTGGTTTATCCCAGATAAAGTATTTCTTA
upper sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G13550.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------------------------------------------------tatatgatt---ctgcaggctcagcactcagtttcaagcctgaattttttatgaaagggattttaacgataacctatgtacacttgtcttttggttct--ttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
||||| | ||| | | | | || | ||| | || | ||| | | | | || | | || || || | ||||||||||||||| |||||||||||||| || ||||| || ||||| ||||||| |||||| || ||||| ||||| ||||||||| ||||| ||| ||
gtaatactactatttttggttagaattcagataaggaaaacgtttattatcttgactgctacttatatagcttgcctgtgtagtaactgttatccgttaaagcagaagtcttct----aattattgttgtgtcatgttgcgtctcccttgtttgtgatttcaatccagGCTTGGATGGCTTATTCGTTTCATTAGTCACTCAGTCATATCTGGATTTACAAGTGCTTCGGCCATTGTGATTGGGTTATCTCAAATAAAATATTTCCTG
upper sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G12520.1 (Arabidopsis thaliana), 3'ss of exon 3
tatatgattctgcaggctcagcactcagtttcaagcctgaattttttatgaaagggattttaacgataacctatgtacacttgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
| | | || || | || |||| |||| | ||| | | | | | | || ||| | |||| |||| | ||||||||||||||| ||||||||||| || || ||||| |||||||| |||||||||||||||||| |||| ||||| ||||| ||| |||||||||| |
-----gtatttatagtctt--ctctttgtttgtgcaaggaatcctgtattttttgtagtgttagaacaagt--tgttcgtttgttttttcaacc---cagGCTTGGATGGCTTATTCGTTTCATAAGTCACTCAGTCATTTCTGGATTTACAACTGCTTCAGCTGTTGTAATTGGGTTATCCCAACTGAAATACTTCCTA
upper sequence: GLYMA18G52270.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv13s0019g00010.t01 (Vitis vinifera), 3'ss of exon 3
-----ta-tatgattctgcaggctcagcactcagtttcaagcctgaattttttatgaaagggattttaacgataacctatgtacacttgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
|| || | | |||| | | | | || || ||| | ||| | |||| | || ||| || ||| | | | || |||||||||||||| ||||||||||| || || || ||||||||||| ||||| || |||||||| ||||| |||| ||||||||||| || || ||| ||
atttgtactagaaatttgcatattttctatcttttaattattctcaaatttctgtgat-gtcatttagaaagaaaatgatgcacccttttttcct-----ttctagGCTTGGATGGCTTATTCGTTTCATCAGTCACTCTGTGATTTCTGGGTTTACGACAGCTTCAGCAATTGTGATTGCCTTATCTCAAGCAAAGTATTTCCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatgaaagggattttaacgataacctatgtacacttgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
tcttttggttctttc CT-rich tract
attttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatgattctgcaggctcagcactcagtttcaagcctgaattttttatgaaagggattttaacgataacctatgtacacttgtcttttggttctttcagGCTTGGATGGCTGATTCGTTTCATTAGCCATTCAGTGATTTCTGGCTTTACAACTGCTTCAGCTATTGTCATTGGTTTATCTCAAGCGAAATACTTCTTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - tgcaggc
- - - - - - - - - - gcactca
- - - - - - - - - - - - - - -ttcaagc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgtac