Sequence
atgc intronic sequence ATGC exonic sequencegtttgtattgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaatttagacttggaattgacatgtgaaattaattattggtagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG
Basic information
species | Glycine max |
transcript | GLYMA14G39170.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G39170.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0079g00600.t01 (Vitis vinifera), 3'ss of exon 3
gtttgtattgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaatttagacttggaattgacatgtgaaattaattattggtagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG
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-------------gtacctatcta--cctacctacattc-attcattcattctctttt-------tctagctgctatctccctccctcat-taactttatgttttggtagATGGGATACTCCAATCCATGTAGATGCAGCAAGTGGTGGCTTTATTGCACCCTTTCTTCACCCAGAGCTGGAGTGGGACTTCCGCTTGCCACTTGTGAAA
upper sequence: GLYMA14G39170.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv01s0011g06600.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtattgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaattta----gacttggaattgacatgtgaaattaattattggtagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG
|| | || | ||| | | | ||| ||| | ||| || | ||| | || | | ||| | || | | | || || | |||||||| || ||||||||||| |||||||| |||||||||||||||||||| || || ||||| || || |||||||| || || | ||| | ||||||
gtatataat-cactcttctaccaacatttag----ttcagaattttgaaatc---tttgaagtcttccgaattaatatgctctgttcctttttttttgtttttttttcctgcagATGGGATACCCCAATTCATGTTGATGCAGCTAGTGGTGGATTCATTGCACCATTCCTTTATCCGGAACTGGAGTGGGACTTCCGCCTTCCATTGGTGAAG
upper sequence: GLYMA14G39170.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ18071 (Selaginella moellendorffii), 3'ss of exon 4
gtttgtattgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaatttagacttggaattgacatgtgaaattaattattgg-------tagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG
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--------------------------------------------------------gtaaaatatctctctgtgttcgtcgagaaaaagcttgaaacttatcgttttcttgccttagATGGGATACTCCTATCCACGTTGATGCTGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG
upper sequence: GLYMA14G39170.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ36644 (Selaginella moellendorffii), 3'ss of exon 4
gtttgtattgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaatttagacttggaattgacatgtgaaattaattattggtagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG
| | ||| | | | | | |||| || | | | || || ||||||| | ||||| || || || ||||| |||||||| |||||||| || || || |||||||| || | |||||||||||||| ||||| || || |||
-------------------------------------------gtaaaagatctctttgtgttcgtcgaggaaaagcttgaaacttttcttt----ttttttggccttagATGGAATACTCCTATCCACGTTGATGCCGCCAGTGGAGGATTCATCGCTCCATTCCTCTATCCAGATTTGGAGTGGGATTTTCGATTGCCTCTTGTCAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttaaggtactttaatttagacttggaattgacatgtgaaattaattattggtagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG
aattaat putative branch site (score: 3)
atgtgaaattaattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtattgcacatattgattgagtcttaactgcttcctattttgtgaacctagtttaaggtactttaatttagacttggaattgacatgtgaaattaattattggtagATGGGACACTCCAATTCATGTGGATGCAGCCAGTGGTGGATTCATTGCACCTTTTCTCTATCCTGAGCTTGAGTGGGATTTTCGGTTGCCACTAGTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT