Sequence
atgc intronic sequence ATGC exonic sequencegtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgaccatttttggtattccaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
Basic information
species | Glycine max |
transcript | GLYMA09G01830.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g10630.1 (Oryza sativa), 3'ss of exon 2
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatat-tgaccatttttggtattccaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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-------------------------------------------------------------------------------------gaaaaaaaactgtattcacctaagaattgactttt-----cctgttcttggggataaat-cataaatgac---aagcatatgtaacctttttccctcttccaatattagGTAGTGATCATGGGGTGAAAGCTCATGGTGATGGTTGGTTGCTGACTGTTGCACTTATTGAGGGAAGCGGTGTAGTAGGTTCAGGTACACCTGGCTTGCC
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os08g38440.1 (Oryza sativa), 3'ss of exon 2
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgaccatttttg-gtattccaatat---tagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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------------------------------------------------------------------------------------------------tttcttcagaaacatatgaacaagtaccaca-ataatgtgatttgcatttcttgatgtagtgcttttcattgttgaatcttacactcacaaatgtgtgcagTTGGTGATCATGGTGTCAAGGCACAAGGTGATGGATGGTTGTTAACAGTTGCCTTAATTGAGGGAACCAAACTGGCTCCAGTTGATGCTACTGGTTTTTC
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os06g19400.1 (Oryza sativa), 3'ss of exon 2
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgaccatttttggtattccaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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-----------------------------------------------------------------------------------ctttagaaaaaccttctattcttgttctggacatatatactcccg--tgatttatgcacatatgaactaaactttgcttacatgg----tatttgggagtata----tagGAAGTGATCATGGAGTCAAAGCACAAGGGAATGGTTGGTTGCTGACTGTCGCTCTGATTGATGGTACCAATTTAGCAGCAACCAAATCATCTGGTTACTC
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G005195_T03 (Zea mays), 3'ss of exon 2
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgacc-atttttggtattccaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC---
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------------------------------------------------------------------------------------------tttatttttctttgat-tcaacaaaacttccaggtttcagatactgttctggataattactc--ttacaatcttccttattgatcttttggattgta-tattagGT---GATCATGGAGTCAAAGCACAAGGGGATGGCTGGTTGCTGACTGTTGCTCTGATGGAGGGAACCAACTTGGCAGCAACCAAATCATCTGGTTACTCTGA
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G03370.1 (Arabidopsis thaliana), 3'ss of exon 2
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgaccatttttggt--attccaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
| | | |||| | || | ||| | | | | || ||| | | | |||| | || | ||| |||| || | |||||| |||| ||||||||||| |||||||| || |||||||| ||||||||||||||||| ||||||| || | | |||| |||| ||| | || ||| |
--------------------------------------------------------------------------------gtaacatccatgaagatacagcatcgaccatttcatattctttcttgcggtctctcattgttagcgtggtgtgttt---atccgactgatcattacatgtcaaatccaattatagGCAGTGATCATGGCATCAAAGCGCATGGAGATGGTTGGTTGCTAACTGTTGCTCTAATTGAGGGGGTCGATCTAGCAGCTGTAGATCCAAGCGGGCATTG
upper sequence: GLYMA09G01830.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0194g00100.t01 (Vitis vinifera), 3'ss of exon 2
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgaccatttttggtattc-caatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
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---------------------------------------------------------------------------------------aaaaaatattgccatattattttctcaaatctgttat-tttattggttttttctt---cttgttggtttaaaatt---ttgactcttttaattgttttcaattttagGCAGTGATCATGGAGTCAAAGCACAAGGAGATGGGTGGCTGCTAACTGTTGCCTTGATTGAAGGCAGTAATTTAGCAGCTGTTGACTCAAGTGGATTCTC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaatgcctgcgtgtctgtaattatattgaccatttttggtattccaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
tattgac putative branch site (score: 2)
tctgtaattatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctcagaatgttcagttacttcacacttcatgaatctggctttcctttttctccctgacttagtgttgcttttaatgaagtgactatgagtttgtcgctcttgtcttttgaatgtttagtgcctattaacttattttaatgcctgcgtgtctgtaattatattgaccatttttggtattccaatattagGTAGTGATCATGGAATCAAAGCACAAGGAGATGGGTGGTTGCTAACTGTTGCCTTAATTGAAGGAAGCAGTTTAGCTTCTGTTGATTCTAGTGGGTTGTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA