Sequence
atgc intronic sequence ATGC exonic sequence...agaagtcactagtaaacagaagaaaacatgcttttgttacagttgtgtgcattggaagcacatttattatgacatttgttatggcattcaaatcttgtagTGTGCTACATCATGTGCATTGGCAGCACACAAATTGCGGCGCCCAGTCAGGATGTATCTAAATCGAAAGACAGATATGATAATGGCTGGAGGAAGGCATC
Basic information
species | Glycine max |
transcript | GLYMA02G44000.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G141535_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------agaagtcacta-gtaaacagaagaaaa-catgcttttgttacagttgtgtgcattggaagcacatttattatgacatttgttatggcattcaaatcttgt-agTGTGCTACATCATGTGCATTGGCAGCACACAAATTGCGGCGCCCAGTCAGGATGTATCTAAATCGAAAGACAGATATGATAATGGCTGGAGGAAGGCATC
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gtaagtcctgcctgtaactagagcttcagttcactcaatattttgtgttttcaattgccactgtattgtcaattgaacttcatgatttgaccaaaaaactgt---tgagatgcaaatg-gtgttagaaatgatcatggattttcctctttgtcagACTGCATGTGCATGTGCCCTTGCTGCCTTCAAGCTGCGGCGTCCAGTTAGGATGTACCTCGATCGCAAGACGGACATGATAATGGCTGGAGGGAGACATC
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 5
lower sequence: AT2G27150.2 (Arabidopsis thaliana), 3'ss of exon 5
agaagtcactagtaaacagaagaaaacatgcttttgttac-agttgtgtgcattggaagcacatttattatgacatttgttatggcattcaaatcttgtagTGTGCTACATCATGTGCATTGGCAGCACACAAATTGCGGCGCCCAGTCAGGATGTATCTAAATCGAAAGACAGATATGATAATGGCTGGAGGAAGGCATC
|| | || | | || || || ||| |||| | | |||| ||| || | | | | | ||| ||| || || || ||| || |||| ||| | | ||| |||| |||| || || || | ||||| | | || || ||||| ||||||||||||||||||||||| ||||
----gtaagtatttaccataat------tggtttctttactggcttcttgcac--gaatcaagatcgtga--atgctcatta--aaatt--gatgtttcagGTTGCAACCGCATGCGCACTAGGCGCATACAAGTTGCAACGTCCTGTTAAGATGTTTTTGAACCGCAAGACGGATATGATAATGGCTGGAGGAAGACATC
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 5
lower sequence: AT1G04580.1 (Arabidopsis thaliana), 3'ss of exon 5
agaagtcactagtaaacagaagaaaacatgcttttgttacagttgtgtgcattggaagcacatttattatgacatttgttatggcattcaaatcttgtagTGTGCTACATCATGTGCATTGGCAGCACACAAATTGCGGCGCCCAGTCAGGATGTATCTAAATCGAAAGACAGATATGATAATGGCTGGAGGAAGGCATC
| | | ||| | || | || || | | | | | ||| | | | || | || || ||| ||| ||||||| | || ||| | ||| ||| ||| || || ||||| || | || || ||||| ||||||||||||||||||||||||||||
-------------------------gtaagtaatagtttc--ttctctgaataaaagtcctttgtgatttgatactaatgctgctgaagatgattt-cagGTTGCGACAGCATGTGCGCTTGCTGCAAAAAAAATGCAGCGTCCTGTAAGGATATACGTCAACCGTAAGACTGATATGATAATGGCTGGAGGAAGGCATC
upper sequence: GLYMA02G44000.3 (Glycine max), 3'ss of exon 5
lower sequence: Vv06s0009g00770.t01 (Vitis vinifera), 3'ss of exon 5
--agaagtcactagtaaacagaagaaaacatgctttt-gttacagttgtgtgcattggaagcacatttattatgacatttgttatggcattcaaatcttgtagTGTGCTACATCATGTGCATTGGCAGCACACAAATTGCGGCGCCCAGTCAGGATGTATCTAAATCGAAAGACAGATATGATAATGGCTGGAGGAAGGCATC
|| | | | | | ||||||| || || | | | | | || ||| | | | || || | ||| ||||||| |||||||| | |||||| ||||||| || ||||| ||| |||| ||| | ||||| || || ||||||||||| || |||||||| ||||
cttgatctgattctgtttcctttaatggtgtgctttttgtcctgtttctttccctcaacaatggcttctaagtgaaaacactcactctat---gatgtcttagGTTGCTACAGCATGTGCACTTGCAGCATACAAATTACGCCGCCCTGTCCGGATATATATGAATCGCAAAACTGATATGATAATAGCAGGAGGAAGACATC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgtgcattggaagcacatttattatgacatttgttatggcattcaaatcttgtagTGTGCTACATCATGTGCATTGGCAGCACACAAATTGCGGCGCCCAGTCAGGATGTATCTAAATCGAAAGACAGATATGATAATGGCTGGAGGAAGGCATC
atttattatgacattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
agaagtcactagtaaacagaagaaaacatgcttttgttacagttgtgtgcattggaagcacatttattatgacatttgttatggcattcaaatcttgtagTGTGCTACATCATGTGCATTGGCAGCACACAAATTGCGGCGCCCAGTCAGGATGTATCTAAATCGAAAGACAGATATGATAATGGCTGGAGGAAGGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - -agaagaaa
- - - - - - - - - - - - -acatgct
- - - - - - - - - - - - - - - - - - - - - -tgtgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcattca