Sequence
atgc intronic sequence ATGC exonic sequence...caatgtcccattttctctcctattatgaattttcttctgtttttcagcagttttttttgttgaaaattatgttgcttacctgaattttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAAAAAATGGTGGTAGCATAATTGGTGGAACTTTCA
Basic information
species | Glycine max |
transcript | GLYMA02G01000.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g18320.1 (Oryza sativa), 3'ss of exon 3
caatgtcccattttctctcctattatgaattttcttctgtttttcagcagttttttttgttgaaaattatgttgcttacctgaattttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAAAAAA-TGGTGGTAGCATAATTGGTGGAACTTTCA
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------------------------gtgtttattgtagtgtgcaattgctgttttgttt-ttgatgattcagataagaatacggtgatttcggtgcttagGTGTGTATGCTGGTGATCCTTCAAAGCTCAGTATGAAGGCTGCATTTGGGAAGGTGTGGAGGCTGGAGGATACTGGAGGTAGCATTATTGGTGGAACCAT--
upper sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G01690.1 (Arabidopsis thaliana), 3'ss of exon 3
---------------------ca-atgtcccattttctctcctattatgaattttcttctgtttttcagcagtttt---ttttgttgaaaattatgttgcttacctgaattttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAA-AAAATGGTGGTAGCATAATTGGTGGAACTTTCA
|| || |||||| || || | | || | ||||||||| ||||||| | | | | | | | ||| | | || | || ||||| || |||||||||||| | || ||||||||||| |||||||| ||||||| || || |||||||||| |||||||| ||||| |||||
gtagagttatagataaaacttcatgtgaaccatttattcatttagatgtcagcgaatctgattatctagcagttttcatttttgttctagtgcacccttaatgctttagattttatgcttttagGTGTTTATGCTGGTGATCCTTCAAAACTGAGCATGAAAGCAGCGTTTGGGAAGGTTTGGAAACTAGAGCAAAATGGTGGAAGCATAATAGGTGGTACTTT--
upper sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g02540.t01 (Vitis vinifera), 3'ss of exon 3
caatgtcccattttctctcctattatgaattttcttctgtttttcagcagttttttttgttgaaaattatgttgcttacct---gaat-tttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAA-AAAATGGTGGTAGCATAATTGGTGGAACTTTCA
|||| | || | | || | ||| | | | | || ||| | |||| | | | | || | | ||| ||| || ||| | | || |||||||| |||||||||||| | || ||||||||||||||||| |||||||||| ||| || | || |||||||| ||||||||||| || ||
--ctgtcaaaagttttatgaagttcacagaattcacc-gactcttgtcattttagatggttgttgctcaggccgatttcattggaaatgttttttgtatgcagGTGTTTATGCAGGAGATCCTTCAAAACTGAGCATGAAAGCAGCATTTGGAAAAGTTTGGAAGCTTGAGCAGAAGGGTGGTAGTATAATTGGTGGCACCTT--
upper sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ23527 (Selaginella moellendorffii), 3'ss of exon 3
caatgtcccattttctctcctattatgaattttcttctgtttttcagcagtttttt-ttgttgaaaattatgttgcttacctgaattttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAAAAA-ATGGTGGTAGCATAATTGGTGGAACTTTCA
| || | | ||| ||| | | ||| | |||| || |||| | | || ||||| || |||||||| ||||| ||||||||||| ||||| |||||||| |||| ||||||| | | ||||| ||||| || || |||||| |
------------------------------------------gtgagtactatttgattggcgtagatt-ttccccttagttggatttc---------agGCGTTTATGCTGGTGATCCTTCGAAATTGAGTATGAAAGCTGCATTCGGGAAAGTATGGAAGCTGGAAGATCAAGGTGGAAGCATCATCGGGGGAACTAT--
upper sequence: GLYMA02G01000.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ34803 (Selaginella moellendorffii), 3'ss of exon 2
caatgtcccattttctctcctattatgaattttcttctgtttttcagcagtttttt-ttgttgaaaattatgttgcttacctgaattttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAAAAA-ATGGTGGTAGCATAATTGGTGGAACTTTCA
| || | | ||| ||| | | ||| | | |||| || |||| | | || ||||| || |||||||| ||||| ||||||||||| ||||| |||||||| |||| ||||||| | | ||||| ||||| || || |||||| |
------------------------------------------gtgagtactatttgattgacgtagattttcct-cttagttggatttc---------agGCGTTTATGCTGGTGATCCTTCGAAATTGAGTATGAAAGCTGCATTCGGGAAAGTATGGAAGCTGGAAGATCAAGGTGGAAGCATCATCGGGGGAACTAT-- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.agcagttttttttgttgaaaattatgttgcttacctgaattttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAAAAAATGGTGGTAGCATAATTGGTGGAACTTTCA
tgcttac putative branch site (score: 2)
ttttgtt putative PPT
ttttttttgttgaaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
caatgtcccattttctctcctattatgaattttcttctgtttttcagcagttttttttgttgaaaattatgttgcttacctgaattttgttatatataagGGTCTATGCAGGCGATCCTTCAAAATTAAGTATGAAAGCAGCATTTGGGAAAGTTTGGAGGCTGGAAAAAATGGTGGTAGCATAATTGGTGGAACTTTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- -tgtccca
- - - - - - - ctctcct
- - - - - - - - - - - - - - - - tcttctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcttacc