Sequence
atgc intronic sequence ATGC exonic sequencegtactgcagatttattttctgaaaatggcagtaccaatgatatctttttccccattgagaatgtctagccatttaaacgtgaccgatgtcactgaacatgcgatattctactataagattgttggtaaccctatttatgatacgtcccggttacttacatcttgtttcatgcttctcgtgtagATTGATAGCGATCTGCGAGGATATATATGCTGCTAGAGCTGAGGGTGAGCTTGGAATTGAAGAGGTCCTTTACTGGACTCTAGTGAAGATATACCGGTCC
Basic information
species | Glycine max |
transcript | GLYMA10G02870.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G02870.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G48060.1 (Arabidopsis thaliana), 3'ss of exon 20
gtactgcagatttattttctgaaaatggcagtaccaatgatatctttttccccattgagaatgtctagccatttaaacgtgaccgatgtcactgaacatgcgatattctactataagattgttggtaaccctatttatgatacgtcccggttacttacatcttgt---ttcatgcttctcg-tgtagATTGATAGCGATCTGCGAGGATATATATGCTGCTAGAGCTGAGGGTGAGCTTGGAATTGAAGAGGTCCTTTACTGGACTCTAGTGAAGATATACCGGTCC
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--------------------------------------------------------------------------------------------gtaacatttgtaaacattgtccaagagttttgctgttcc-----atgatac-tctcaacctctaagagattatgaccactcactgttgaatgtagATTAATAGCCATATGCGAGGACTTGTACGCGGCTAGAGCAGAGGGTGAGCTTGGAGTAGAAGAAGTTCTATACTGGACGCTTGTGAAGATCTATAGATCC
upper sequence: GLYMA10G02870.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0104g00760.t01 (Vitis vinifera), 3'ss of exon 20
gtactgcagatttattttctgaaaatggcagtaccaatgatatctttttccccattgagaatgtctagccatttaaacgtgaccgatgtcactgaacatgcgatattctactataagattgttggtaaccctatttatgatacgtcccggttacttacatcttgtttcatgcttctcgtgtagATTGATAGCGATCTGCGAGGATATATATGCTGCTAGAGCTGAGGGTGAGCTTGGAATTGAAGAGGTCCTTTACTGGACTCTAGTGAAGATATACCGGTCC
| | | || || || | || | | | ||| | | | || | | || |||| | | || |||||| || ||||| |||||||| ||||| ||||||||||||||||| || | ||||||||||||||| | || ||| | || ||||||||||| |||||||| ||| ||||
-------------------------------------------------------------------------cttgctttatcgttg-cattcaaacta----aacccacttcataaatattca-agttatgcttgagataactgataactttccccaacttgttc----attacgatgtagGTTGATAGCCATCTGTGAGGATATATATGCTGCAAGGTCAGAGGGTGAGCTTGGAGTGGAGGAGATTCTCTACTGGACTCTGGTGAAGATCTACAGGTCT
upper sequence: GLYMA10G02870.1 (Glycine max), 3'ss of exon 4
lower sequence: EFJ35512 (Selaginella moellendorffii), 3'ss of exon 27
gtactgcagatttattttctgaaaatggcagtaccaatgatatctttttccccattgagaatgtctagccatttaaacgtgaccgatgtcactgaacatgcgatattctactataagattgttggtaaccctatttatgatacgtcccggttacttacatcttgtttcatgctt-ctcgtgtagATTGATAGCGATCTGCGAGGATATATATGCTGCTAGAGCTGAGGGTGAGCTTGGAATTGAAGAGGTCCTTTACTGGACTCTAGTGAAGATATACCGGTCC
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---------------------------------------------------------------------------------------------------------------------gtctgtgctgatc--gattttcatgcttttcgcttgcgttaagtcgaccgcttcttcgctttcgcagATTGATAGCGATCTGCGAAGATATATACGCGGCACGCGCTGAAAGAGAACTGGCACTGGAAGAAGGATTGTTCTGGACGCTG------------------ atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccctatttatgatacgtcccggttacttacatcttgtttcatgcttctcgtgtagATTGATAGCGATCTGCGAGGATATATATGCTGCTAGAGCTGAGGGTGAGCTTGGAATTGAAGAGGTCCTTTACTGGACTCTAGTGAAGATATACCGGTCC
tacttac putative branch site (score: 1)
tgcttctc putative PPT
tttatgata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtactgcagatttattttctgaaaatggcagtaccaatgatatctttttccccattgagaatgtctagccatttaaacgtgaccgatgtcactgaacatgcgatattctactataagattgttggtaaccctatttatgatacgtcccggttacttacatcttgtttcatgcttctcgtgtagATTGATAGCGATCTGCGAGGATATATATGCTGCTAGAGCTGAGGGTGAGCTTGGAATTGAAGAGGTCCTTTACTGGACTCTAGTGAAGATATACCGGTCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA