Sequence
atgc intronic sequence ATGC exonic sequencegtaatctcagtcttatctatagctctactactgtgtatgttgcttgacctttgtgagggcttttctgtttgcaaatttgtttaagcagtgtttttttttttttttataaataatccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
Basic information
species | Glycine max |
transcript | GLYMA19G42340.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os08g32600.1 (Oryza sativa), 3'ss of exon 6
gtaatctcagtcttatctatagctctactactgtgtatgttgcttgacctttgtgagggcttttctgtttgcaaatttgtttaagcagtgtttttttttt--tttttataaataatccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
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----------------acagggttctgttgcttgttgtgt-gtttaaa---tgcaggatcatccctactgttacgttccacatgtttatatttttctttcacatgctattaccttttcagGCGACCACT------GCCAAGACAATGAAAGGGACACCATATTGGATGGCCCCAGAAGTAATTGTTGGGAGTGGGCATGACTT
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G064613_T03 (Zea mays), 3'ss of exon 6
gtaatctcagtcttatctatagctctactactgtgtatgttgcttgacctttgtgagggcttttctgtttgcaaatttgtttaagcagtgtttttttttttttttataaataatccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
| || ||| | || ||| | | || | || | | | | || || | || || || ||| || | || | | | | ||||||| ||| ||||||| | ||||||||||| |||||||||||||| |||||||| ||| | | || || |
---------gcattcattattgaccttttaccatct--gtcatccgtccatcatata---tcatgtgcttttatccttcaatac-cactgtaattccatgcttgtct---tctgctagGCAACTGCAACTGCTGCCAAGACGATGAAAGGTACCCCATATTGGATGGCACCAGAAGTCATTGTTGGAAGCGGTCACAATTG
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G09000.1 (Arabidopsis thaliana), 3'ss of exon 6
gtaatctcagtcttatctatagctctactactgtgtatgttgcttga------cctttgtgagggcttttctgtttgcaaatttgtttaa-gcagtgttttttttt------ttttttataaataa------------tccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
|||| | || || | | |||| |||| |||| || | || || | | | | ||| | || || || | | | || ||| | | | | | || |||| || || ||||||| || || |||||||| || ||||||||||||||||| ||||||||||| || ||||| ||| ||||
gtaagtcaaaaaata---atttgttttctacaaagtatattgcaggaagcattctgttctgtgtattctcttatttcttagttggtctagtataacatatccttcagagtgatttaatgtgattgacttgatttcatctctagGCTACGATGACTGGTGCAAAATCTATGAAAGGGACACCATATTGGATGGCTCCGGAAGTTATTCTTCAAACTGGACATAGCTT
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 6
lower sequence: AT1G54960.1 (Arabidopsis thaliana), 3'ss of exon 6
------------gtaatctcagtcttat-ctatagctctactactgtgtatgttgcttg--acctttgtgagggcttttctgtttgcaaatttgtttaagcagtgtttttttttttttttataaataatccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
|| |||| ||| | || || || | | || | || | || | | ||||| | | | | || | | || | | || | || |||| || ||||| |||||||| || |||||||| ||||| |||||||||||||||||||||||||| || || |||||| ||||
gtaagtcaatttttagtctccaacttctacttcagtaaaaccattctgctctcagttttctagtcttattcaagtttttcatataatatactccttatcatgatttcgattaatatacttgagttttctctagGCTACTATTTCGGGTGCCAAATCTATGAAAGGAACTCCCTATTGGATGGCTCCAGAAGTTATTCTTCAAACCGGGCATAGCTT
upper sequence: GLYMA19G42340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv14s0128g00430.t01 (Vitis vinifera), 3'ss of exon 6
gtaatctcagtcttatctatagctctactactgtgtatgttgcttgacctttgtgagggcttttctgtttgcaaatttgtttaagcagtgtttttttttttttttataaataatccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
||| | | ||| ||| | | | | | | | | ||| | ||||||| |||| || | || | || | | || || | |||| |||||||| |||||||||||||||||||| || || |||||||||||||| ||||| ||||||||||| || ||| ||||
gtacacactatctgctctgtgtttattcatttattcagttgacttaatttttgtgattacttt--tgctcaaaatctcgtctgattgagacattggttgccat-------------agGCTACCATTTCAGGTGCCAAGTCCATGAAAGGCACCCCGTATTGGATGGCTCCGGAAGTCATTCTCCAGACAGGCCATAGCTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgtttgcaaatttgtttaagcagtgtttttttttttttttataaataatccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
aaatttgtttaagcag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatctcagtcttatctatagctctactactgtgtatgttgcttgacctttgtgagggcttttctgtttgcaaatttgtttaagcagtgtttttttttttttttataaataatccagGCAACCATTTCTGGTGCCAAGTCCATGAAAGGTACTCCATATTGGATGGCTCCAGAAGTTATTCTCCAGACTGGGCATTGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT