Sequence
atgc intronic sequence ATGC exonic sequencegtaagctttatttctggttcctttactttgccatttagttcctcaacaaagaatgcagtatatatgcagcattcgtgatcatcagcttcattaagttacagaaattaactcgcattttgtaattgagacgtaagctaagttcttttcatgattcatattgaagttcaacgtgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
Basic information
species | Glycine max |
transcript | GLYMA02G48050.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g44015.1 (Oryza sativa), 3'ss of exon 7
gtaagctttatttctggttcctttactttgccatttagttcctcaacaaagaatgcagtatatatgcagcattcgtgatcatcagcttcattaagttacagaaattaactcgcattttgtaattgagacgtaagctaagttcttttcatgattcatattgaagttcaacgtgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
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-------------------------------------------------------------------------------gattttcttgtatgagtaatataagt------atgttgtctatttagtttgtag--tggtttcctttttt--ttccttttcc--ctaaacagtcttt---ctcttgggttgcca----gATTTGAACCTGATATGCTTGCATTTTCGGGGTGCTATTATGGTGGTGGAGAAAAAGAAAGAAAAGAGCTTGGTGCAATACGGAAGAGATGGAAAACCTTG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os09g37590.1 (Oryza sativa), 3'ss of exon 10
gtaagctttatttctggttcctttactttgccatttagttcctcaacaaagaatgcagtatatatgcagcattcgtgatcatcagcttcattaagttacagaaattaactcgcattttgtaattgagacgtaagctaagttcttttcatgat---tcatattgaagttcaacgtgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
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-----------------------------------------------------------------------------------------------------aagtagagactaaaataacatttcatatgtacactcttcctcttgcactatgcatcattttgctctttttttcagcatgcaccgtctatcctgatggcagGTTTGAACCTGACATGCTTGCCTTTTCTGGGTGTTATTATGGTGGTGGAGAAAAGGAGAAAAGAGAACTAGGCTCCATTCGCAAGCGATGGAAAACTTTG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G142664_T01 (Zea mays), 3'ss of exon 7
gtaagctttatttctggttcctttactttgccatttagttcctcaacaaagaatgcagtatatatgcagcattcgtgatcatcagcttcattaagttacagaaattaactcgcattttgtaattgagacgtaagctaagttcttttcatgattcatattgaagttcaacgtgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
| | || || | | | || | || |||| || || |||| ||| || | | || | | | | | || ||||| || || |||||||| |||||||||||||| |||||||||||||| | |||| || |||||||| || ||| | || ||||||| | |
-------------------------------------------------------------------------------------------------------gtgacatcagatctctttgctttcttgt----tcagcacttt--gtgtttgatat-atagtgcacactaactctgatgacccatctgttg-acagATTTGAGCCTGACATGCTTGCTTTCTCTGGTTGCTACTACGGCGGTGGAGACATTGAGAGAAGAGAACTTGGTGAGATTCGTAAGAGGTGGAAGACCCTG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G131699_T01 (Zea mays), 3'ss of exon 7
gtaagctttatttctggttcctttactttgccatttagttcctcaacaaagaatgcagtatatatgcagcattcgtgatcatcagcttcattaagttacagaaattaactcgcattttgtaattgagacgtaagctaagttcttttcatgattcatattgaagttcaacgtgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
||||| | | || || || | | | | || | | ||||| | | | | | | | | || | || || ||||| ||||||||||| || || || ||||||||||| |||||||| ||||||| | |||||||| | || ||||| |||||||| ||
-----------------------------------------------------------------------------------------------ttacaaataccttttctcagcgcatatgcgtttcctttac--ggtaatgatattgattttttcttgtccctttcttaaacattattccttttgcaatgt-cagATTCGAACCTGATATGCTTGCCTTTTCGGGGTGCTATTACGGTGGTGGAGAGAAAGAGAGGAGAGAACTTGGTGCTATAAGGAAGAGGTGGAAAGGCTTG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G168614_T01 (Zea mays), 3'ss of exon 6
gtaagctttatttctggttcctttactttgccatttagttcctcaacaaagaatgcagtatatatgcagcattcgtgatcatcagcttcattaagttacagaaattaactcgcattttgtaattgagacgtaagctaagttcttttcatgattcatattgaagttcaacgtgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
| | | || ||||| || | | ||| ||| || | |||| || |||| | ||| | ||| || || || | |||| | || |||||||| || |||||||| || ||||| |||||||| || ||||||||||| |||| | ||| | | | |||| | | ||| |||| || ||
--------------------------------------------------------------------------------gtgaaatatatcttgttacttc--tttattactattccgtac----aacattagctcgttttgtttc-tatttcttgaccaag----acatggtt------gttgttctgatg-gcagATTTGAACCTGACATGCTTGCCTTTTCTGGGTGCTATTATGGTGGTGGAGAAAAGGAGAGGAGAGAATTAGCTGCAATTCGCAGACGATGGAGAACCTTG
upper sequence: GLYMA02G48050.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv03s0038g03240.t01 (Vitis vinifera), 3'ss of exon 7
gtaagctttatttctggttcctttactttgccatttagttcctcaacaaagaatgcagtatatatgcagcattcgtgatcatcagcttcattaagttacagaaattaactcgcattttgtaattgaga--cgtaagctaagttcttttcatgattcat---attgaagttcaacg--tgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
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---------------------------------------------------------------------------------------------------------gtatatggtttttgaaatagggaaacttggttttgattgtattccagctgcattgaacagggttttcatggatttttcttatggatgttcattgtcatagGTTTGAACCTGATATGCTTGCATTCTCTGGATGCTATTATGGTGGAGGAGAAAAAGAAAGGACAGAACTGGGCGCATTAAGGAAGAGGTGGAAAACTTTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttcatgattcatattgaagttcaacgtgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
aactgat putative branch site (score: 3)
ttttatc CT-rich tract
attcatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagctttatttctggttcctttactttgccatttagttcctcaacaaagaatgcagtatatatgcagcattcgtgatcatcagcttcattaagttacagaaattaactcgcattttgtaattgagacgtaagctaagttcttttcatgattcatattgaagttcaacgtgattcaaactgatgttttatcacatagGTTTGAACCGGATATGCTTGCATTCTCTGGTTGCTATTACGGCGGTGGAGAAAAAGAGAAAAAGGAACTTGGCGAAATTAGGAAACGGTGGAAAAATTTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA