Sequence
atgc intronic sequence ATGC exonic sequence...aacatgaatggatgatacatggtttctgtagtttcttgtaattaaaacatgtagacttttcagaatcattggtctaacaatgacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
Basic information
species | Glycine max |
transcript | GLYMA15G07800.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os04g44710.2 (Oryza sativa), 3'ss of exon 3
aacatgaatggatgatacatggtttctgtagtttc--ttgtaattaaaacatgtag-acttttcagaatcattggtctaacaa--tgacttg----tgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
| | || || | || ||| | | || || ||||| | |||| || || | | ||| || | | || |||| | ||||| |||||||| || |||| || ||||||||||| ||||||||||||||| | | ||||||||| ||||| ||||||||||| | ||| |
---------gagcgctaagcacttcccgtctattcagctttgatacaaccatgttccatgtttccatgctgttatactgcctagttgattttccctttttcttaattagATAAGAGATACCAGTGTTCTGGTACGGTTGAGGCCTGCATGGGAGGATCTTCGGAGCTACTTAATTGCAAGAGGTCGCAAACGTTTTGAGGTATATGTGT
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g42600.1 (Oryza sativa), 3'ss of exon 2
-aacatgaatggatgatacatggtttctgtagtttcttgtaattaaaacatgtagactttt-cagaatcattggtctaacaatgacttgtgtctt---tggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
| | || | | |||| | || | || | || | || || || | || || | |||| | || | | || || |||| | ||||| ||||||||||| | ||||| || |||||||| ||||| ||||||||| ||| ||| ||||| ||||| ||||||||||| | ||| |
cagcgtgcct---tttcacattgctttgat-gtggcctg-actttggttgcataagtttgtacaaaacttccaggctaaggctttttttttttttttttgtgtagATAAGGGATACCAGTGTTCTTGTACGTTTAAGGCCAGCATGGGAGGATCTCCGGAGCTACTTGATTGCTAGAGGTCGCAAACGTTTTGAGGTCTATGTGT
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G120373_T01 (Zea mays), 3'ss of exon 2
aacatgaatggatgatacatg-gtttctgtagtttcttgtaattaaaacatgtag----acttttcagaatcattggtctaacaatgacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
|| | | || | |||| || | | || || || | ||| | | || ||||| ||| | || || |||| ||||| | ||||| ||||| ||||| | ||||| || || ||||| |||||||| |||||| | | ||| ||||| ||||||||||||||||| | ||| |
--gattctttgttgttgcatgtagttttcaaccttgtttggatctgattttgttgcacaaaaattgtcaatcagctatctgattttgttctg---ctttctgcagATTAGGGATACCAGTGTGCTTGTATGTTTAAGGCCAGCCTGGGAGGATCTTCGCAGCTACTTAATTGCCAGAGGTCGCAAGCGTTTTGAGGTCTATGTGT
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G21670.1 (Arabidopsis thaliana), 3'ss of exon 2
aacatgaatggatgatacatggtttctgtagtttcttgtaattaaaacatgtagacttttcagaatcattg-gtctaacaatga---cttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
| || | || | | ||| | | || || | | | || |||| ||||| |||| ||| | || | || | | | | | | ||||||||||||| |||||||||||||| | || || ||||||| || ||||| ||||| |||| |||| |||||| ||||||||||| || | |||||
--cttgtg-gtataaccttttattttt-catttgctcctttctggagcacctagatttttctgaattcttgtggctgaatctgcattcctatatttacacacagATTCGTGATACAAGTGTTCTTGTGAGAATGAGGCCCTCATGGGAGGAACTTCGAAGCTATTTGACAGCAAAAGGGCGTAAGCGTTTTGAAGTATATGTTT
upper sequence: GLYMA15G07800.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv00s0370g00040.t01 (Vitis vinifera), 3'ss of exon 2
--aacatga-atggatgatacatggtttctgtagtttcttgtaattaaaacatgtagacttttcagaatcattggtctaacaatgacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
| || | | | | ||| || || || | | | | ||| | | | | || || | | || | ||| | ||||||||||||| ||||| ||||||||| |||||||||||||||| || || ||||||||||| |||||||| |||||||||||||||||||||| |||||
ataccactatacttcttgtttatgtcatccaataagcctgtaaactcattccaagaaactggtttgt-ttagtgacacaaaatttttttatatctcc--acagATTCGTGATACAAGTGTACTTGTGAGGCTAAGACCTGCATGGGAGGACCTCCGGAGCTACCTAACTGCAAGGGGGCGCAAGCGTTTTGAGGTTTATGTTT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacatgtagacttttcagaatcattggtctaacaatgacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
gtctaac putative branch site (score: 2)
tgtcttt putative PPT
aatcatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aacatgaatggatgatacatggtttctgtagtttcttgtaattaaaacatgtagacttttcagaatcattggtctaacaatgacttgtgtctttggaaagATTCGTGATACTAGTGTTCTTGTGAGGTTAAGACCTGCATGGGAAGATCTTCGGAGCTACCTGACTGCAAGAGGGCGCAAGCGTTTTGAGGTTTTTGTTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- catgaat
- - - - - - - - - - -gtttctg
- - - - - - - - - - - - - - - - - - - - - - - acatgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caatgac