Sequence
atgc intronic sequence ATGC exonic sequence...gtattgattaacacagtgtaaagataggttttgaaatattgattagttcattttaatttttcttctgatttagcgttttattacttggatctacaatcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
Basic information
species | Glycine max |
transcript | GLYMA16G02770.1 |
intron # | 19 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 19
lower sequence: LOC_Os07g23990.2 (Oryza sativa), 3'ss of exon 17
gtattgattaacacagtgtaaagataggttttgaaatattgattagttcattttaatttttcttctgatttagcgttttattacttggatctacaa-tcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
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-aatgaattgttcctgttctttgttaactgtctacttcctgtagaatgtaattaactgagacacatctgtaagggattaaccttttctatttttaaattagGTATGTCAAGCGTGCACTATATCTACTGCATCTTACATGCGGGCCATCTCATCCAAACACAGCTGCGACATATATCAACGTAGCTATGATGGAGGAAGGC
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 19
lower sequence: AT1G01320.1 (Arabidopsis thaliana), 3'ss of exon 19
gtattgattaacacagtgtaaag-ataggttttgaaatattgattagttcat---tttaatttttcttctgatttagcgttttattacttggat-ctacaatcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
||| | ||| ||| | | | | | | | | || | ||| | ||| || | |||| || | || | | | |||||||| |||||||| || ||||| | ||||| ||||| || |||||||||||||| ||||||||||| ||||| ||||| || |||||||| ||||||
gtaa-gtttagcactcttgattttaaaagaatcgcgaggttagatggtttaaatgtttgatgtctctttccatcatctaaacctggatatgattgtttttgttagGTATGTTAAGCGTGCGTTGTATCTCTTACATCTCACATGCGGTCCATCTCATCCAAATACTGCTGCTACATACATCAATGTAGCCATGATGGAGGAAGGT
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv15s0046g00740.t01 (Vitis vinifera), 3'ss of exon 19
gtattgattaacacagtgtaaaga--taggttttgaaatattgattagttcattttaatttttcttctgattta-gcgttttattacttggatctacaatcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
|| | | | | ||| | | | | || || | ||| || | | |||||| | | || | || ||||| ||||| || || || | |||||||||||||| || ||||||||||||||||||||||||||||| || || || ||||||||||||||||| |||||
---ttaagcgatgtaagacacagaattctatactagcctgtttatccatggcctttttgcttccatttgatttttacccctggccacatttttcattgatcagATATGTAAAACGCGCGCTGTATCTTCTGCATCTCACTTGTGGCCCATCTCATCCAAACACTGCTGCGACATATATCAATGTGGCTATGATGGAGGAAGGC
upper sequence: GLYMA16G02770.1 (Glycine max), 3'ss of exon 19
lower sequence: Vv00s0388g00080.t01 (Vitis vinifera), 3'ss of exon 4
gtattgattaacacagtgtaaaga--taggttttgaaatattgattagttcattttaatttttcttctgattta-gcgttttattacttggatctacaatcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
|| | | | | ||| | | | | || || | ||| || | | |||||| | | || | || ||||| ||||| || || ||| | |||||||||||||| || ||||||||||||||||||||||||||||| || || || ||||||||||||||||| |||||
---ttaagcgatgtaaaacacagaattctatactatcctgtttatccatggcctttttgcttccatttgatttttacccctggccacatttttcattgatcagATATGTAAAACGCGCTCTGTATCTTCTGCATCTCACTTGTGGCCCATCTCATCCAAACACTGCTGCGACATATATCAATGTGGCTATGATGGAGGAAGGC atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttcattttaatttttcttctgatttagcgttttattacttggatctacaatcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
ttctgat putative branch site (score: 3)
ttttaatttttcttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattgattaacacagtgtaaagataggttttgaaatattgattagttcattttaatttttcttctgatttagcgttttattacttggatctacaatcagGTATGTGAAGCGTGCTTTATATCTTCTGCATCTAACATGTGGCCCATCTCATCCAAACACTGCTGCTACTTACATTAATGTGGCTATGATGGAAGAAGGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - ggttttg