Sequence
atgc intronic sequence ATGC exonic sequencegtaagtttttctgttttgttctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
Basic information
species | Glycine max |
transcript | GLYMA05G34850.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g50040.1 (Oryza sativa), 3'ss of exon 1
gtaagtttttctgt--------tttgttctgaaagggtaata--ggtagagaaa-atgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
||| || || || || | | | | ||| || ||| || | || ||||| |||| | |||| | | |||||||||||| ||||||||||||||||||||| |||||| | ||||||||||| |||||||||||| || |||| || |||||||| | ||||||| |
gtacgtattctcgtcctataacttggcgttaagaatgtactactggtgaagcagcattgtgatttgtgag--taacctgctgtggccgcgtgt-agGTGGACTTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTGATGTCGTGGGGGCTGATCGACT
upper sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g14540.1 (Oryza sativa), 3'ss of exon 1
-----------------------------------gtaa-gtttttctgttttgttctgaaagggtaata--ggtagagaaaatgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
|| || | | |||| || | ||||| | | ||| | || | | |||| || | | ||||||||| ||| |||||||||||||||||||| |||||| | ||||||||||| |||||||||||| || |||| | |||||||| | ||||||| |
gtacggaccaccaccgctctctctctctctctgttctagcattaatgcggtttgcaatgtagtagtaatgatgacgatgtcgctgacggtttcttggaatggtggcgtggcgtggcgtggcagGTGGACCTGACGGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGGCTGATCGACT
upper sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G076049_T01 (Zea mays), 3'ss of exon 1
--------------------------gtaagtttttctgttttgtt---------ctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttct--cagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
||| | ||| | | ||| | | || ||| | || | | | | |||| || | | |||||||| ||| ||||||||||||||||||||| |||||| | ||||||||||| |||||||||||| || |||| | |||||||| || ||||||| |
gtacgtgcaccgacccagtccgactaataaatcactctctatagttgccttttggcctatagagtaccgttgaagcaagacatgtgtgagcattaccgcgccatttggtcgtcgcgtaacagGTGGATCTGACCGGAGGGTACTACGACGCCGGCGACAACGTGAAGTTCGGGTTCCCGATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G455642_T02 (Zea mays), 3'ss of exon 1
----------------------gtaagtttttctgttt----------tgttct-gaaagggtaataggtagagaaaatgatgattaatgag---gttggtacattgtgtttttttct-cagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
|||| | | || | || | | | ||| || | | | | |||||| | | | | || | | || ||||||||| ||| || |||||||||||||| || |||||| | ||||||||||| || ||||||||| || |||| | |||||||| || ||||||| |
gtctgtctctctctctctttcagtaatccctcccattcatgcgcacaccatcctcgtatgcgtacgcacgagcgcattgcgtcagtaatgaacacgcacgcatgctctgctgtgcactgcagGTGGACCTGACGGGCGGGTACTACGACGCGGGCGACAACGTGAAGTTCGGGTTCCCTATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G455642_T01 (Zea mays), 3'ss of exon 1
----------------------------------gtaagtttttctgttt----------tgttct-gaaagggtaataggtagagaaaatgatgattaatgag---gttggtacattgtgtttttttct-cagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
|||| | | || | || | | | ||| || | | | | |||||| | | | | || | | || ||||||||| ||| || |||||||||||||| || |||||| | ||||||||||| || ||||||||| || |||| | |||||||| || ||||||| |
gtacggacgggagtctgtctctctctctctttcagtaatccctcccattcatgcgcacaccatcctcgtatgcgtacgcacgagcgcattgcgtcagtaatgaacacgcacgcatgctctgctgtgcactgcagGTGGACCTGACGGGCGGGTACTACGACGCGGGCGACAACGTGAAGTTCGGGTTCCCTATGGCGTTCACGGCGACGCTCATGTCGTGGGGCCTGATCGACT
upper sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G70710.1 (Arabidopsis thaliana), 3'ss of exon 1
gtaagtttttctgttttgttctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
|||||| | || | | | | || | | || ||| | || | |||||||| ||||| ||| || |||||||||||||| |||||||| |||||||| ||||||||||||||| | || || ||||| || ||||| | |||||||
gtaagtcta-ctctactaacatacatttcaaacttctccttcttctaatctctaacttttccgacg-atatttcaaaaatctcagGTTGACTTATCCGGTGGTTACTACGACGCCGGAGACAACATCAAGTTCGGTTTTCCGATGGCGTTCACAACAACGATGCTTTCATGGAGTATAATCGATT
upper sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S376_19V6.1 (Physcomitrella patens), 3'ss of exon 1
------------------------------------------------------------------gtaagtttttctgttttgt-tctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttct-cagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
| | | | ||| | || | | | | |||| | | | ||| ||| || ||| | || | ||||| || ||||| ||||||||||||||||| || |||||| | ||||||||| |||| ||||| ||| | ||| |||| ||| | | | | || |
gtatgctaaatagattcttccagaagtagaggcagaaactttacgcagcaatttcattgcaaattcatgtgcctgtacactttttatccgcgaaattggacctctgctgaaattgtaaa-attgaccttgacg-atggtggactcttgtgcagGTTGATTTGAGTGGAGGGTACTACGACGCGGGAGACAACGTTAAGTTCGGGCTTCCAATGGCATTCAGCGTCTCCATGTTGTCTTGGGGAGCGGTGGAGT
upper sequence: GLYMA05G34850.1 (Glycine max), 3'ss of exon 1
lower sequence: EFJ08014 (Selaginella moellendorffii), 3'ss of exon 1
-----gtaagtttttctgttttgttctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
|| | || || | ||| || | | || | | | | || | | ||| | | | |||||||| | | | ||||| |||||||| |||| |||||| | ||||| || || |||||||||||| ||| || ||||||||||||||||| | || |
gtaccatagaatcttttgctc-gtttgaaatgtttttcttgtg--------gtttacctttctagtcgatcgattttcgctgctgctcagGTGAATCTCACGGGAGGCTACTACGATTCCGGCGACAACGTCAAGTTTGGCTTCCCGATGGCGTTCACGATCACGCTGCTGTCGTGGAGCGTGGTGGAAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
gattaat putative branch site (score: 3)
ttgtgtttttttctc putative PPT
aaaatgatgattaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtttttctgttttgttctgaaagggtaataggtagagaaaatgatgattaatgaggttggtacattgtgtttttttctcagGTGGACTTGAGCGGAGGGTACTACGACGCCGGGGACAACATAAAGTTCGGGTTTCCGATGGCGTTCTCGACGACAATGCTGTCGTGGAGCGTGATCGATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG