Sequence
atgc intronic sequence ATGC exonic sequence...gcatgttataaatttacgaacggggattgatgcgcatatttgagtttatttttgtgactgtatttttatttcttttggtgtttcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAGATGCCTAGATTTATCA
Basic information
species | Glycine max |
transcript | GLYMA15G18980.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os09g27230.1 (Oryza sativa), 3'ss of exon 4
gcatgttataaattt-acgaacggggattgatgcgcatatttgagtttatttttgtgactgtatttttatttcttttgg--tgtttcctcgtatttggt-gcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAGATGCCTAGATTTATCA
|| | || | | || || || | || | ||| || | | | || | || | | || || ||| | |||| ||||| | ||| | ||||||||||| || |||||||||||||| ||||| || || ||||||||||| || | |||
---tgcttgaatctccatgatcgaagaatt-tggaagcaactgaattgctagctactagcagatgatcatggaaagagacttaattattctctcttgcttgcagCCGAGAGAGGTTCAGCGAGATGCATGCCAGGCTATGGTGGGAAGAAAACCGAGCGAGGATACATGAACAGTATCTCTGA---------------------
upper sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os08g36020.1 (Oryza sativa), 3'ss of exon 4
gcatgttataaatttacgaacggggattgatgcgcatatttgagtttattt--ttgtgactgtatttt-tatttcttttggtgtttcc-tcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAG-ATGCCTAG-ATTTATCA
|| | | ||| | || | | || | | | | | | || | || || || || | ||| ||||| || | |||||| || || || || | |||||||| || || |||||||||||||||||||| || || |||||||| || || | |||| |||| | || |||
---tggcagagattcatgagcatctgctcatttg-gtttcgcaatacacttagtcgttcctctaaagaacatgtatttatctgttttggctgttctgcgtgcagCCGGGAGAAATTCAGCGAGATGCACGCCAGGCTATGGTGGGAAGAGAACCGGGCAAGGATACATGATCAGTATCTCTGAGAAGACATGCTAATCATGTAT--
upper sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G429658_T01 (Zea mays), 3'ss of exon 5
------------------------------------------------------------------gcatgttataaatttacgaac-ggggattgatgcgcatatttgagtttatttttg-tgactgtatttttatttcttttggtgtt-tcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCT-AGATGCCTAGATTTATCA
| | || || ||| | | | | | | | | || | |||| | | | ||| | | | || | ||| || ||| ||| || || ||||| | |||| |||||| ||||||||||||||||||||||| || || ||||| ||||||||| | |||| | | ||| |||
gtttgtgacccatgatgcttcagagccctttccactagcttgctcttagaataaacttgctatgtataacatgatcaacttaaaatcagagaagctagccacctacatagaattatacaagattgcagtagatacacgattgtttacatggcccttgtgcttg---cagCCGGGAGAAGTTCAGCGAGAGGCATGCCAGACTATGGTGGGAAGAGAACCGAGCGAGGATACACGAACAATACCTCTGAGAAGAAACGCCCGAGACCATC-
upper sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G066672_T01 (Zea mays), 3'ss of exon 5
----------------------------------------------------gcatgttataaatttacgaacggggattg-----atgcgcatatttgagt----ttattt----ttgtgactgtatttttatttcttttggtgtttcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCT-AGATGCCTAGATTTATCA
| | | || ||| | | | || | | || | | || | |||| ||| | | | ||| || ||| ||| || ||| ||| || || ||||| | ||||||||||| || || ||||||||||||||||| || || ||||| ||||||||| | |||| ||| ||| |||
gtttgtgtccagcgctcttcccactagcttgctcttaggacaaacttgcaaggtacaagagtaacttaaaagcagagaaggcacctaagccttcactggaataggattatacaagattgcagcagatacatgattgtttacaatgtc-ccttgtgcttg---cagCCGGGAGAAGTTCAGCGAGATGCATGCCAGGCTGTGGTGGGAAGAGAACCGAGCGAGGATACACGAACAATACCTCTGAGAAGAGACGCCCGACACCATC-
upper sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 3
lower sequence: AT5G20540.1 (Arabidopsis thaliana), 3'ss of exon 4
gcatgttat-aaatttacgaacggggattgatgcgcatatttgagtttattt-ttgtgactgtatttt-tatttcttttggtgtttcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAGATGCCTAGATTTATCA
| | | ||| || | || |||| | | | | |||||| | | ||| | | || || ||| | || | | ||||| ||||| | || ||||||||||| || ||| ||||||||||||||||| | || || ||||||||||||||||||||| | | | ||| || |
--gtactgttaaacttccttac----attgtctca-aaacccgggtttatccatcggttctgaactaaacatcactcaaactgtgttttcttttgcattgcagCCGAGAGAGATTCGGGGAGATGCACGCGAGATTATGGTGGGAAGAGAACAGGGCAAGGATACATGAACAATACTTGTGATCATAAATCTAAGAGTTTTGT
upper sequence: GLYMA15G18980.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv11s0016g01460.t01 (Vitis vinifera), 3'ss of exon 5
--gcatgttataaatttacgaacggggattgatgcgcatatttgagtttatttttgtgactgtatttttatttcttttggtgtttcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAGATGCCTAGAT-TTATCA
|||| | || || | | | | | ||| | | || | | | | ||| | | | | | |||||||||| |||||| |||||| ||||||||||||||||| |||||||| |||||||| || |||||||||||||| ||||||||| || | | || | |||
cagcatatctcaa--ttcctgccttttaccatttccaatagggaattacatggactttgagctgaaccccctgttcttgttttatatgcatttttggtgcagCCGAGAACGGTTTGGAGAGATGCATGCTAGACTTTGGTGGGAGGAGAACCGGGCAAGAATACATGAACAGTACTTGTGAAGGAGCTAACCAGGGATCATC- atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatttttgtgactgtatttttatttcttttggtgtttcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAGATGCCTAGATTTATCA
tgtatttttatttctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgttataaatttacgaacggggattgatgcgcatatttgagtttatttttgtgactgtatttttatttcttttggtgtttcctcgtatttggtgcagTCGAGAAAAGTTTGGGGAGATGCATGCTAGACTATGGTGGGAAGAGAACCGTGCCAGAATACATGAACAATACTTGTGAGCTAGATGCCTAGATTTATCA
gcatgtt
- - - - - - - - - - - gggattg
- - - - - - - - - - - - - - - - - - - - - - - - - - -gtgactg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgtttcc