Sequence
atgc intronic sequence ATGC exonic sequencegttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
Basic information
species | Glycine max |
transcript | GLYMA12G31330.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G074262_T01 (Zea mays), 3'ss of exon 4
gttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
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------------------------------------gttggttcttcatgaacatgcttctgtat-ttgccttttatttggttccgtcctctgttacctcaac-gcatgagttttga---------tagGGCTGCTATGTTTGCATTGTGACGGGATACTGTGAAGGTGGCGATAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 3
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 3
gttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
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--------------------------------gtaagttttacatcactttgatttttatgg--atttaaagtagatttggtta-aaggattttgataggagctagatttga--------aaaatgcagGGTTGCTATGTTTGTATTGTCACTGGATACTGTGAAGGAGGAGACAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 3
gttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
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-------------------------------------gta---ggtcctggaaattctagttttttgacgaatttttttgctgtaaatgcgaccttgtactgaatcgagagctttgggttggaatgcagGGTTGCTATGTTTGCATTGTCACTGGATATTGTGAAGGAGGAGACAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 3
gttagagaaagcacaccgtttcaattgttatattgcagt---atgcagtaatg-tactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
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-----------------gtatgagcttgtacagggtgaataaatccagtaatggtactgtct-ctataaactt--gtgagtggaagaacagtgcataactttt-----acatgtgttttt-----tgcaacagGGATGCTATGTATGCATCGTTACAGGTTACTGTGAAGGTGGTGACAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ32716 (Selaginella moellendorffii), 3'ss of exon 3
gttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
| | ||||| | | | | || || | | || ||| |||| |||| |||||||||||||| ||||||||||| |||||||| || || ||
---------------------------------------------------------------------gtgagtgttgctctttgatctgttcagcttatggactataa----ctggatgta--acagGGATGCTATGTTTGCATCGTTACTGGATATTGTGAAGGGGGTGATAT
upper sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 3
lower sequence: EFJ20709 (Selaginella moellendorffii), 3'ss of exon 3
gttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
| | ||||| | | | | || || | | || ||| |||| |||| |||||||||||||| ||||||||||| |||||||| |
---------------------------------------------------------------------gtgagtgttgctctttgatctgttcagcttatggactataa----ctggatgta--acagGGATGCTATGTTTGCATCGTTACTGGATATTGTGAAGGGG------- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
ttgtaac putative branch site (score: 2)
tttttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttagagaaagcacaccgtttcaattgttatattgcagtatgcagtaatgtactttctgctgtaaactggagtttgttggattgtaacgtttttctttttggctgtgtatgtttttggttgtattgtagGGTTGCTATGTTTGCATTGTTACTGGATACTGTGAAGGTGGAGACAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA