Sequence
atgc intronic sequence ATGC exonic sequencegtaattactctcaccatgtactagaaatgaagtggtggcagatgtgctaaaacatctaggctaactgttcgcaattttttctttctcttcttgatttatccagacttaggtgattcttagttctgaccatgcaattgacttgacatattatatgatatccattggaggtattattttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
Basic information
species | Glycine max |
transcript | GLYMA15G07340.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os01g57350.2 (Oryza sativa), 3'ss of exon 6
gtaattactctcaccatgtactagaaatgaagtggtggcagatgtgctaaaacatctaggctaactgttcgcaattttttctttctcttcttgatttatccagacttaggtgattcttagttctgaccatgcaattgacttgacatattatatgat-atccattggaggtattattttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
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--------------------------------------------------------------------------------------gtatgccacaagcttggaattagttgatc---gaatctga--atgatactttcttggc-tctcatctcaccatttagggataataataatacatttcagGTTTGGTGGCTGATATAGATATTGAGTCTGAGAAGTACAGGTGGATGGGAAGTGCACGCTTTGATTTCTAT
upper sequence: GLYMA15G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os07g37580.2 (Oryza sativa), 3'ss of exon 5
gtaattactctcaccatgtactagaaatgaagtggtggcagatgtgctaaaacatctaggctaactgttcgcaattttttctttctcttcttgatt-tatccagacttaggtgattcttagt-tctgaccatgcaattgacttgacatattatatgatatccattggaggt-attattttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
|| ||| || | | ||||| || || | |||| || | | | || || | ||| | | | | || || | || | | | || | | | | | | ||| | | | |||||||||| || ||||| || |||||||| || |||||| |||||||||| ||||||||||| || || |||
----------------------------------gtatgccgtgtattagc---ttgatgctaagctttt----ttctctcttaaactacacgtctatacccccataacactgactgtcactctcagagcttgttctcccactatctatttctggggcactaagagaaaacgatttatgaactgcagGTCTGGTAGCTGATATCGATATTGAGTCAGAGAAGTACAGGTGGATGGGCAGTGCTCGTCTTGACTTCTAT
upper sequence: GLYMA15G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G057475_T03 (Zea mays), 3'ss of exon 6
gtaattactctcaccatgtactagaaatgaagtggtggcagatgtgctaaaacatctaggctaactgttcg----caattttttctttctcttcttgatttatccagac-ttaggtgattcttagttctgaccatgcaattgacttgacatattatatgatatccattggaggtattat-tttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
| | || || |||| ||||||| || | ||| | | | || |||| || || | ||| ||| | | || | | | ||| | | || | | ||| | | | ||||||||||||| ||| |||| ||||| || || ||||| ||||||||||||||||||| || || ||||||
-------------------------------------gtatgcagcatataatttctatgctaactatttgaaaacaacagctgagaacacagaccaccttcctcagagattgctccatcactttctcttttgccgcagtaaaatttaattgacaactgacaagc-ctgaaaatgatatatgaactgcagGTCTGGTGGCTGATGTTGATATTGAATCGGAGAAGTATAGGTGGATGGGAAGTGCTCGCCTTGAATTTTAT
upper sequence: GLYMA15G07340.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv00s0181g00250.t01 (Vitis vinifera), 3'ss of exon 6
--gtaattactctcaccatgtactagaaatgaagtggtggcagatgtgctaa-aacatctaggctaactgttcgcaattttttctttctcttcttgatttatccagacttaggtgattcttagttctgacc-atgcaattgacttgacatattatatgatatcc-attggaggtattattttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
| | | | ||| | ||| | | || ||| | || | || || || |||||| | || || || ||| || | |||| || |||| || | || | | | || | ||| | |||| ||||||||||||||||||||||||||||||||||||| || |||||||||||||||||||| ||||||| ||
gtatgaccaaaatttccaccacttgtttatgccatactcttggaactgcaagtgactgttgaactgg--atttttaagacaagctttctaagaat-atgcctctggatttactagaataagctttctagtggatttgtttgattttgatagctctactttgccttactgacagaattttagtattccagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAATATAGGTGGATGGGAAGTGCTCGTTTAGATTTCTAC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcaattgacttgacatattatatgatatccattggaggtattattttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
ttttatttc CT-rich tract
tattattttatttca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattactctcaccatgtactagaaatgaagtggtggcagatgtgctaaaacatctaggctaactgttcgcaattttttctttctcttcttgatttatccagacttaggtgattcttagttctgaccatgcaattgacttgacatattatatgatatccattggaggtattattttatttcagGTCTGGTGGCAGATATTGACATTGAGTCTGAAAAGTACCGGTGGATGGGAAGTGCTCGTCTAGATTTTTAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA