Sequence
atgc intronic sequence ATGC exonic sequence...tatgaaacaagccttatgtgacatttagaagttgttatttcatcccatggaaacttggctatttgcattttaaacaccctttgctataattcatattcagGAGATCCATTCTTTAAGAGCACAACTGGAAGCAGCCAAATATGATGTCATAAAATACTGCATAGGAACACTTGTTTCGATCTCTGCTGTTGGTCTTGCTG
Basic information
species | Glycine max |
transcript | GLYMA17G17170.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G17170.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os06g49890.1 (Oryza sativa), 3'ss of exon 6
tatgaaacaagccttatgtgacatttagaagttg-ttatttcatcccatggaaacttggctatttgcattttaaacaccctttgctataattcatattcagGAGATCCATTCTTTAAGAGCACAACTGGAAGCAGCCAAATATGATGTCATAAAATACTGCATAGGAACACTTGTTTCGATCTCTGCTGTTGGTCTTGCTG
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--------gtgagtaaagtggccttcatgtgtgggctctgttatctcactg----tcgggcattaacagggtttgtctgatttgctactgttgg----cagGAAATTCACTCACTGAAAGCCCAGCTCGAGGCAGCAAAGTATGATGTCATCAAGTACTGCATAGGTACCATTGTTTCGATATCAGCTGTTGGACTCGCCG
upper sequence: GLYMA17G17170.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g02670.t01 (Vitis vinifera), 3'ss of exon 1
tatgaaacaagccttatgtgacatttagaagttgttatttcatcccatggaaacttg-gctatttgcattttaaacaccctttgctataattcatattc--agGAGATCCATTCTTTAAGAGCACAACTGGAAGCAGCCAAATATGATGTCATAAAATACTGCATAGGAACACTTGTTTCGATCTCTGCTGTTGGTCTTGCTG
| || ||| || | | || || | ||| || | || || | | | | | ||| | | | ||| ||| || || ||||||| ||| | ||| || ||| | ||||| | || |||||||||||||||||||||||| | || |||||||| || || ||| | | ||||||
-agctaagaagtgtttttcattacttggatat--ctatgagattcaatctttgtttttgttttctaaagttttttcgggttgtcttatttttcttaatcctagGAGATTCATGCACCAAGGGCTCAATTAGAAGCTGTAAAGTATGATGTCATAAAATACTGCATAAGTACCCTTGTTTCTATTTCAGCTATGGAGGTTGCTG
upper sequence: GLYMA17G17170.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g02920.t01 (Vitis vinifera), 3'ss of exon 6
--------tatgaaacaagcctt-atgtgacatttagaagttgttatttcatcccatggaaacttggctatttgcattttaaacaccctttg-------ctataattcatattc--agGAGATCCATTCTTTAAGAGCACAACTGGAAGCAGCCAAATATGATGTCATAAAATACTGCATAGGAACACTTGTTTCGATCTCTGCTGTTGGTCTTGCTG
|| | || | ||| || | | ||| | || | || ||| | | |||| || |||| || | | | ||| || || |||| || ||| | |||| || || ||||||| || || || ||||| ||||||||||||||||| || |||||||| || || ||||| ||||||||||
gtgagtatcataagtgtagttgagaagtgtttttcattacttggatatctatgaggttcaatctttgtt-tttgttttctaaagtgttttcgggttgtcttctttttcttaatcctagGAAATTCATGCACTAAGGGCTCAGTTGGAAGCTGCAAAGTACGATGTGATAAAATACTGCATAGGTACCCTTGTTTCTATTTCAGCTGTGGGTCTTGCTG
upper sequence: GLYMA17G17170.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv04s0023g02930.t01 (Vitis vinifera), 3'ss of exon 7
---tatgaaacaagccttatgtgacatttagaagttgttatttcatcccatggaaacttggctatttgcattttaaacaccctttgctataattcatattcagGAGATCCATTCTTTAAGAGCACAACTGGAAGCAGCCAAATATGATGTCATAAAATACTGCATAGGAACACTTGTTTCGATCTCTGCTGTTGGTCTTGCTG
| ||||| | | || || || || | || | || || | ||| | || |||| |||| | ||||| || ||| | |||| || || | ||||| || || |||||||| ||||||||||||||||| || |||||||| || || ||||| |||||| |||
gtgagtatcacaagtgtagttggatatctatgaggttcaatctttgtttttgttttctaaagttttttcgggtt--gttttctttttcttaatcc-----cagGAAATTCATGCACTAAGGGCTCAGTTAGAAGCTGCAAAGTATGATGTGATAAAATACTGCATAGGTACCCTTGTTTCTATTTCAGCTGTGGGTCTTACTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catggaaacttggctatttgcattttaaacaccctttgctataattcatattcagGAGATCCATTCTTTAAGAGCACAACTGGAAGCAGCCAAATATGATGTCATAAAATACTGCATAGGAACACTTGTTTCGATCTCTGCTGTTGGTCTTGCTG
tatttgcattttaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatgaaacaagccttatgtgacatttagaagttgttatttcatcccatggaaacttggctatttgcattttaaacaccctttgctataattcatattcagGAGATCCATTCTTTAAGAGCACAACTGGAAGCAGCCAAATATGATGTCATAAAATACTGCATAGGAACACTTGTTTCGATCTCTGCTGTTGGTCTTGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- -gaaacaag
- - - - - -ccttatg
- - - - - - - - - - - - - - - - - - - - catccca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattt