Sequence
atgc intronic sequence ATGC exonic sequencegtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
Basic information
species | Glycine max |
transcript | GLYMA19G45050.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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----------------------ctgtgttgtattatttgataggtctgcatttgta-agctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatt---tgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 3
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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--------------------gtctgtaatcaaa--------cactgtatttatacactcacgtcagggaccatatgctctgtggaact-----tttttaccatttgggctcttgt----tgtacagGTTGATCGGGTCTTGTACTCGTCAGTGGTTTACCCCCACAACTACGGCTTCATCCCTCGAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGC
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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----------------------------------------gtaatgtgacttcccaaagatt------gtgatcttcttttctt--ttaactgttctgatg--gatgacattgaatttgatctcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgattt-ttttcctataccca--tctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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---------------------------------------gttagatgagaacaaagtttattttttatatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattctc--tcattca--gGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCA
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
lower sequence: AT4G01480.1 (Arabidopsis thaliana), 3'ss of exon 4
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
||| || | | | | | | | | | | || ||| | || | | ||| | || | ||||||||| || || | ||||| || ||||| ||||| || ||||| || ||| |||| |||||||| |||||||||||||| || || |||||||| |||
---------------------------------------------gtaaaaagatatcaaatcttgaaa-aaacagaatgatctgaggatatatgatgatcgtaagtgtttgtatatgtctatcagGTTGATAGGATTCTTTATTCTTCGGTTGTGTATCCTCACAACTACGGGTTTGTCCCACGCACACTATGTGAAGACAATGACCCTATAGATGTTTTAGTTA
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
----------------------------gtacaaaccaattgcc---tgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcc-----tatacccatctatctt-----tatgcttacgatttctgaata---attcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
| || || || || ||||| || | || || | | | | | || | |||| ||||| || || || ||| | | | || | ||| | || | || | ||||| || || || || |||||||| || || ||||| ||||||||||| || || || || || || |||||||||||||||||| | |||||||| | |
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatgatgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
upper sequence: GLYMA19G45050.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ27171 (Selaginella moellendorffii), 3'ss of exon 2
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
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--------------------------------------------------------------gtgtgaatagtttgatcttttctttcg-cta-ctttccagttatgctttggtcgttcttc-cagGTTGATCGAGTCCTTTATTCCTCGGTGGTTTATCCACACAACTATGGATTTGTTCCACGCACGCTGTGTGAAGACAATGACCCGCTTGACGTTCTTGTGA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
tgcttac putative branch site (score: 2)
atttctgaataatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacaaaccaattgcctgattactgtaatggaagcccttactgctgtagcttgaaacagattttccagatgatttttttcctatacccatctatctttatgcttacgatttctgaataattcacagGTTGATCGGGTTTTGTATTCATCAGTTGTTTATCCACATAACTATGGTTTTATCCCTCGCACACTGTGTGAAGACAATGATCCAATTGATGTTTTGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA