Sequence
atgc intronic sequence ATGC exonic sequence...cctgtgcaatagtgccattattgctttattttccatttgtacccatagctgaaatttgattcagattctcttaactatcggaatttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTTGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
Basic information
species | Glycine max |
transcript | GLYMA02G09080.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g05260.1 (Oryza sativa), 3'ss of exon 1
-------------------------------------------------cctgtgcaatagtgccattattgctt---tattttccatttgtacccatagc----tgaaatttgattcagattctcttaactatcgga-atttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTTGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
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gtacctggtgttgaagaagcttgcagctactaatatgcataaaaaaacatgaattctttgtttccaggattgcttttatgatttccttaagagcatccaactttgtgataaatagttgaagcttgcttgctcactaattgccttatctgggaggaagGTTCAAGGCCACTGATGCCAATAGGCTTCGTGCTGAATACAACAGGCTGGTTGATGGATTGGCACAGAGGGGAAACCTGCCAA
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G097605_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------cctgtgcaatag-tgccattattgctttattttccatttgtacccatagctgaaatttgattcagattctcttaactatcggaatttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTTGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
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gtaccactcccaattgttggatatacttaagccagccaccaatagccactgaacgataggtcctgtttctttagaactattcatcttcaactttg--tgatggatagttaagcttgctttgccaactg---ctttatctggtaggaagGTTCAAGGCCACCGATGCCAATAGGCTTCGTGCTGAATACAACAGACTGGTGGATGGACTGGCACAGCGAGGAAATCTACCAA
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: AT1G03190.2 (Arabidopsis thaliana), 3'ss of exon 2
----------cctgtgcaatagtgccattattgctttattttccatttgtacccatagctgaaatttgattcagattctcttaactatcggaatttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTTGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
|| ||||| | | | | | || | | | | || | | | | ||| | ||| | || | || |||||||||||||||||||||| ||||||||||| ||| | || |||||||||||| |||| ||||| ||||| ||||| ||||| ||| | |||
cataattttcttggttcaatacaggaa--gtgacctggttatttgctgatgcttatttttaagttcttatt-acattattgaaattgtcc-------aactggtaggaagGTTCAAGGCTACTGATGCAGGAAGATTGCGAGCTGAATACAACCGGCTGGTTGAGGGTTTAGCACTGAGAGGGGACTTATCTG
upper sequence: GLYMA02G09080.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0104g00060.t01 (Vitis vinifera), 3'ss of exon 2
--------cctgtgcaatagtgccattattgctttattttccatttgtacccatagctgaaatttgattcagattctcttaactatcggaatttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTTGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
|| | || | | |||| || ||| | | ||| | | |||| |||| | ||| ||| | || | | |||| |||||||||||||||||||||||||||| |||||| | | || |||||||||||||||||||| |||||||| | || ||| || | |||
ttcactaatttgcagattactact-ttatgttgtttcttttcttctgtcattagaaatgaagtttgttacag-ttcattaaattgt------ttgacatggtaggaagGTTCAAGGCCACTGATGCGGGTAGATTGAGAGCAGAATACAACAGGCTTGTTGAGGGTTTGGCCCAGAGGGGAAACTTACCTA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagctgaaatttgattcagattctcttaactatcggaatttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTTGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
tcttaac putative branch site (score: 2)
aaatttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cctgtgcaatagtgccattattgctttattttccatttgtacccatagctgaaatttgattcagattctcttaactatcggaatttgaactggtaggaagGTTCAAGGCCACTGATGCAGGTAGACTCCGTGCTGAATACAACAGGCTTGTTGAAGGTTTGGCACTAAGAGGAGACCTGCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
cctgtgc
- - - - - - tgccatt
- - - - - - - - - - -tgcttta
- - - - - - - - - - - - - - - - ccatttg
- - - - - - - - - - - - - - - - - - - - acccata