Sequence
atgc intronic sequence ATGC exonic sequencegtaagttaattactattatgtagaggtttgttttttgtttattatgatagtgagtgtaattgtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
Basic information
species | Glycine max |
transcript | GLYMA03G32160.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 5
gtaagttaattactattatgtagaggtttgttttttgtttattatgatagtgagtgtaattgtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
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gttagtagctagcaaatgtgccaacaatcattagaaacttcttcagaattcacctgttattccttgtgtcattatc-tatttctcaatgcattcagaattttcgtt---tccatgttt-tgactggcagt---taatgatttcagGCATACTCCACTGTCGGTACACCGGACTACATTGCTCCAGAAGTTCTTCTAAAAAAGGGTTATGGAATGGAGTGTGATTG
upper sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
gtaagttaattactattatgtagaggtttgttttttgtttattatgatagtgagtgtaatt--gtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
|| || | || |||| | || | | | || ||| | | ||| ||| | | | | ||||| || | || |||||||| |||||||||||||| |||||||| ||||| |||||||||||| ||||||| || |||||||||||||||||||||||
---------------------------------------catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactttatttttttctgt-------aatgttcatattcgaac-ttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
-----------------------------gtaagttaattactattatgtagaggtttgttttt-tgtttattatgatagt-gagtgtaat---tgtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
|| || || | || || |||| || ||| | | | | | | |||| | | | | | | | | | || |||| || | ||| | | || | || | | | | | | ||||||||||| || || || || ||||| ||||| ||||| ||||| || ||||| ||||||||||||||||| ||||| ||
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctccatgatgttctactactctttgagcatcta-gttttcaggttttgacacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
upper sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
gtaagttaattactattatgtagaggtttgttttttgtttattatgatagtgagtgtaattgtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
| | || ||| || ||| ||| || | || | | ||| | | ||||| ||||| ||||| || || ||||||||||||||||| ||||||||| |||| ||||| || |||||||| ||||||||
------------------------------------------------------------------------------------gtgcgtagcttgtacttccttt-tgtcccgattttt--atctaagtgttc---tttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG
upper sequence: GLYMA03G32160.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
gtaagttaattactattatgtagaggtttgttttttgtttattatgatagtgagtgtaattgtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
| | || ||| || ||| ||| || | || | | | | | | ||||| ||||| ||||| || || ||||||||||||||||| ||||||||| |||| ||||| || |||||||| ||||||||
------------------------------------------------------------------------------------gtgcgtagcttgtacttccttt-tgtcccgattttt--atctaagtttcc---tttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
taaatgtgaatgtata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagttaattactattatgtagaggtttgttttttgtttattatgatagtgagtgtaattgtaattcttgaaattatacttacttaatcatctagtattttttttgtgtgtatgcttgtaaatgtgaatgtataaatattgcagGCGTATTCTACTGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTATTGAAAAAGGGTTATGGGATGGAATGTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
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