Sequence
atgc intronic sequence ATGC exonic sequencegttagtgttttaacctaaggttctaatagagattctacttttcatatatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
Basic information
species | Glycine max |
transcript | GLYMA10G34480.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os06g30460.3 (Oryza sativa), 3'ss of exon 5
gttagtgttttaacctaaggt-tctaatagagattctacttttcatatatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
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gttaggattttgctctgggatatttcataa------tagaattgaaacatcttgtttccaattcagagt-tctttatttcttttttat----atattagtttcgatcaaaagttatctgttgtttgcagATAGAAGTTGGTGATGTGATCTGTGAGATAGAAACTGACAAAGCTACGCTTGAGTTTGAGAGCCTTGAAGAGGG
upper sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G52200.1 (Arabidopsis thaliana), 3'ss of exon 10
gttagtgttttaacctaaggttctaatagagattctacttttcatatatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
| || |||| | || | | | | | || ||| ||| | | || || | ||| ||| | | | | ||| | | | | || || ||||||||||||||||||||| | || ||||||| ||||| |||||||| || || |||||||| || |||||||||||
--------------gttagtttctggt---gacccgatgagtaaattggcattgtaa--tttcaccacaagaa-atctgatgtttatgcacttgcctgtgttgattcttc--tcatttcatgaaacagATTGAAGTGGGTGATGTCATAGGTGAGATCGAGACTGACAAAGCCACTCTGGAATTTGAAAGCCTTGAAGAGGG
upper sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 6
lower sequence: AT3G52200.2 (Arabidopsis thaliana), 3'ss of exon 6
------------------------------------gttagtgttt-taacctaaggttctaatagagattctacttttcatatatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctga---acatttaatttatca-aacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
|| ||| | | | | ||||| ||| ||| | | || ||| |||| | | | | | |||| | | || | | | | |||| || || |||| | || ||||||||| || ||||||||||||||||||||||||| || | ||||||||||||| || || ||
gtgggttatttcttatttttggttgacaaaatttcagtcgacttttatgattttgtctactaatgatcattatacaagaaagacgataaattgataatttagctggcaaaga-aaatatagaatgtggaaattctcagtaacaggtatgaatttggttcttcctgacagGTAGAGGTGGGTGATGTACTATGTGAGATAGAGACAGACAAAGCCACTGTAGAATTTGAGAGTCAAGAGGAAGG
upper sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 6
gttagtgtttt-----aacctaaggttctaatagagattcta-cttttcatatatatttttaatat---tttaaaatgtgagcatgag------tcg-ttaatggg--catatatt--ttttgtctgaacatttaat----ttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
|| ||| | | || | | | | |||| || | ||| | | | ||| |||| | |||| ||| || || || || ||| | ||| | || ||| ||| |||| | | ||| |||||||||| ||||| | |||| || |||||||||||||||||||| ||||| ||||| ||||||||||||||
gtcagttatattcaaaaagttgatatgatgtgagagtttaaagcttcttaagttccaatttgatataattataaataatgacaataagaaattttcacttgatgagaccatttgttgatttcatctatgaatttggtgatttaatctaacagATTGAGCCAGGTGACGTTCTATGCGAAATAGAGACAGACAAAGCTACCCTTGAGTTTGAAAGTCTTGAAGAGGG
upper sequence: GLYMA10G34480.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv13s0074g00150.t01 (Vitis vinifera), 3'ss of exon 10
gttagtgttttaacctaaggttctaatagagattctacttttcata-tatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
|| | ||| || | ||| | ||| | || || ||| ||||| ||| || | | || | || | || | | | || ||| |||||| || ||| ||||||| |||||||||||| | ||||||||||||||||||||||||| || ||||||||||| ||||||||||||||
----gtttgttatgcttaa---ttaaaggttattgaatttcaagtaatattttttttcctgtttggaaaata--cttgtttatctattcagcctttcctgttctcttgatcatttacttgatctaacagATAGAAGTGGGTGATGTGATATGTGAGATAGAGACAGACAAAGCCACCCTTGAATTTGAAAGTCTTGAAGAGGG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
atttaat putative branch site (score: 4)
atatattttttgtctg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagtgttttaacctaaggttctaatagagattctacttttcatatatatttttaatattttaaaatgtgagcatgagtcgttaatgggcatatattttttgtctgaacatttaatttatcaaacagATTGAAGTGGGTGATATATTATGTGAGATAGAGACAGACAAAGCTACACTTGAATTTGAGAGTCTTGAAGAGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG