Sequence
atgc intronic sequence ATGC exonic sequence...tttcacaatatgcatatttatatattggaaaattgtttgtcagacatcagttgttgatattttttgcatgcattgataagtagcattgttcctattttagGTTTTACTTAGTCAATGCCATCGGTTTCGGGCTTTAGTACTCCTTGGAAGGTTCCTTGATATGGGGCCATGGGCAGTAGATCTG
Basic information
species | Glycine max |
transcript | GLYMA09G41510.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 10
lower sequence: AT3G08850.1 (Arabidopsis thaliana), 3'ss of exon 10
----tttcacaatatgcatatttatatattggaaaattgtttgtcagacatcagttgt-tgatattttttgcatgcattgataagtagcattgttcctattttagGTTTTACTTAGTCAATGCCATCGGTTTCGGGCTTTAGTACTCCTTGGAAGGTTCCTTGATATGGGGCCATGGGCAGTAGATCTG
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atggcttaggaacattctttggcttccttcaggacgttctatcata-attttgtttgcatattgccattttagcgtatttatag--aatctggtt--tgtttcagGTGTTACTTAGCCAGTGCCATCGGTTTCGTGCTCTTGTACTTCTTGGAAGATTTCTTGATATGGGTTCATGGGCTGTGGATCTG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv08s0058g00890.t01 (Vitis vinifera), 3'ss of exon 10
tttcacaatatgcatatttatatattggaaaattgtttgtcagacatcagttgttgatattttttgcatgcattgataagtagcattgtt-cctattttagGTTTTACTTAGTCAATGCCATCGGTTTCGGGCTTTAGTACTCCTTGGAAGGTTCCTTGATATGGGGCCATGGGCAGTAGATCTG
| | | | | | | | ||| | || || || | | || ||| ||| | | | || | || | |||||||||||| |||||||||||||| ||||| || | || || |||||||| |||||||||||||| |||||||| |||||||||
tgtgtatttcttcctccccttgaaaaaagaaaaagaaaatcttttattt-tttccgcttttctttacatagaataacggataatccaactgtctgtcttagGTTTTACTGAGTCAATGCCATCGATTTCGAGCGCTGGTGCTTCTTGGAAGATTCCTTGATATGGGACCATGGGCTGTAGATCTG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ28980 (Selaginella moellendorffii), 3'ss of exon 10
tttcacaatatgcatatttatatattggaaaattgtttgtcagacatcagttgttgatattttttgcatgcattgataagtagcattgttcctattttagGTTTTACTTAGTCAATGCCATCGGTTTCGGGCTTTAGTACTCCTTGGAAGGTTCCTTGATATGGGGCCATGGGCAGTAGATCTG
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-------------------------------------------------gtccacgttgcttatcctaagcctt---------ttttgtgttttcaacagGTTCTTTTAAGTCAATCTCATCGTTTTCGGGCTTTGGTACTTTTAGGAAGGTTCTTGGATATGGGGGCATGGGCTGTGAACCTG
upper sequence: GLYMA09G41510.1 (Glycine max), 3'ss of exon 10
lower sequence: EFJ13684 (Selaginella moellendorffii), 3'ss of exon 9
tttcacaatatgcatatttatatattggaaaattgtttgtcagacatcagttgttgatattttttgcatgcattgataagtagcattgttcctattttagGTTTTACTTAGTCAATGCCATCGGTTTCGGGCTTTAGTACTCCTTGGAAGGTTCCTTGATATGGGGCCATGGGCAGTAGATCTG
|||| || | ||| |||| | ||||| | | ||||||| ||||| ||||||||||| ||||| | ||||||||| | ||||||||| ||||||| || | |||
--------------------------------------------------------------gttgcttgtcct---aagcctttttgtgttttcaacagGTTCTTTTAAGTCAATCTCATCGTTTTCGGGCTTTGGTACTTTTAGGAAGGTTCTTGGATATGGGGGCATGGGCTGTGAACCTG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atcagttgttgatattttttgcatgcattgataagtagcattgttcctattttagGTTTTACTTAGTCAATGCCATCGGTTTCGGGCTTTAGTACTCCTTGGAAGGTTCCTTGATATGGGGCCATGGGCAGTAGATCTG
cattgat putative branch site (score: 4)
ttcctatttt putative PPT
ttgttgatatttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttcacaatatgcatatttatatattggaaaattgtttgtcagacatcagttgttgatattttttgcatgcattgataagtagcattgttcctattttagGTTTTACTTAGTCAATGCCATCGGTTTCGGGCTTTAGTACTCCTTGGAAGGTTCCTTGATATGGGGCCATGGGCAGTAGATCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - tgcatat
- - - - - - - - - - - - - - - - -tgtttgt
- - - - - - - - - - - - - - - - - - - - - - - - -gttgttg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcatgca