Sequence
atgc intronic sequence ATGC exonic sequence...tttgtttggtacaattttttttcccagatgcaacacttattttgggacggagggacctctaaattccagtatatctgctaacagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
Basic information
species | Glycine max |
transcript | GLYMA08G20140.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g63590.1 (Oryza sativa), 3'ss of exon 4
tttgtttggtaca------attttttttcccagatgcaacacttattttgggacggagggacctctaaattccagtatatctgctaacagaaattagtgact-gcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
| | | | | | ||| || || | | | | | | || | ||| | ||| | || | || ||||| ||| | || || |||||| || || ||||| || ||| ||||||| ||||| || || |||||||| ||| |||| |||||||| ||||| ||||| ||||||||||| ||||| |
tccatatagcatattgttgattcttcttgtgatgatcgaaagcttgtatgtatttcatggag---tgaatg--aatacttttgttaacataaa--aatgccttgcagGTCATAGACTTCCACCAGACATTGGAAGTTAATGGCATACGCTTCTGGTGCTATACTGCTGGCCATGTACTTGGCGCTGCAATGTTCATGGTGGACATTG
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G422649_T01 (Zea mays), 3'ss of exon 4
tttgtttggtacaattttttttcccagatgcaacacttattttgggacggagggacctctaaattccagtatatctgctaa--cagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
| | | | ||| | | | || | | || || || | | ||| || | |||||||||||||||||||| || ||| ||||||| ||||| || || |||||||| || |||| |||||||| |||||||| || |||||||||||||| || |
-ctttaaagca-aatgcaggattctgctcatcatgtttgaaattgagaggctatttttcagggaatacacatttttattaatctgaaagtcgtcttctgcagGTTATTGATTTCCACCAGACATTGGAAGTTAATGGGATACGCTTCTGGTGCTACACTGCTGGCCATGTGCTTGGTGCCGCCATGTTCATGGTTGATATTG
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G083346_T01 (Zea mays), 3'ss of exon 4
tttgtttggtacaattttttttcccagatgcaacacttattttgggacggagggacctct----aaattccagtatatctgctaa--cagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
| ||| || | | | | || | |||| | || | | | | || || | | ||| || || |||||||||| |||||||| || || ||||||| ||||| || || |||||||| || |||| |||||||| |||||||| |||||||||||||| || || |
-tactttaaagaaaatgcagaattctgct----catcttgtttgaaagagactatttttttcagggaatgca-catttttattaatctgaaagttgtcttgtgcagGTTATAGATTTCCACCAGACGTTGGAAGTTAATGGGATACGCTTCTGGTGCTACACTGCTGGCCATGTACTTGGTGCCGCTATGTTCATGGTGGATATTG
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: AT1G61010.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------tttgtttggt-acaattttttttcccaga-tgcaacacttattttggga------cggaggga----------cctctaaattccagtatatctgctaacagaaattagtga------ctgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
| | || | || || ||| | | || ||| |||| ||||||| | | | | | || ||| | | | | ||| || ||| || |||| ||||| |||||||||||||| ||||||||||| || ||||||||||| | ||||||||||| | ||||| || ||||| ||||| || ||||
gttagtactgcattatattctatgactatgtttatactttgactgctccactaggtttgggataagttcaaaagaaattaaatctgcttcaaaactgtgattgttgagttaaggtttatatttgatttcctctatagGTAATTGACTTCCATCAAACAGTTGAAGTGAATGGCATAAAGTTCTGGTGTTACACGGCAGGCCATGTTTTGGGTGCAGCCATGTTTATGGTGGATATAG
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g00170.t01 (Vitis vinifera), 3'ss of exon 4
-tttgtttggtacaattttttttcccagatgcaacacttattttgggacggagggacctctaaattccagtatatctgctaacagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
||||||| | | | | || ||| | | ||| | || ||| ||| || | |||||||||||||||||||||||||| | ||||| |||||||| | ||| |||||||| | | |||||||||||| ||||||| ||||| |||||||| || |
gaatgtttggccatttacaaaaattgacttaaggtatgtagtttaattttatcatctcatttaatcttcctgtaactg-taattaaatctcccttctgcagGTTATTGATTTCCATCAAACTTTAGAAGTAAATGGTATACAATTTTGGTGTTACACAACTGGCCATGTCCTTAGTGCTGCCATGTTTATGGTTGATATTG
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g00030.t01 (Vitis vinifera), 3'ss of exon 4
------tttgtttggtacaattttttttcccagatgcaacacttattttgggacggagggacctctaaattccagtatatctgctaacagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
| | ||||| || |||| |||| ||| | | ||| | || ||| ||| || | ||||||||||||||||||||||| || | ||||| |||||||| ||||| |||||||| | || ||||| |||||||||||||| ||||| |||||||| || |
gaatgttgggccatttacaacaattgactttagatatgtagcttaatttta-----ttatctcatttaatcttcctgtaactg-taattaaatctcccttctgcagGTTATTGATTTCCATCAGACTTTAGAAGTAAATGGTATACGATTTTGGTGTTACACAGCTGGCCACGTCCTTGGTGCTGCCATGTTTATGGTTGATATTG
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv12s0035g00190.t01 (Vitis vinifera), 3'ss of exon 4
------tttgtttggtacaattttttttcccagatgcaacacttattttgggacggagggacctctaaattccagtatatctgctaacagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
|| | || || || ||||| |||| ||| | | ||| | || ||| ||| || | ||||||||||||||||||||||| || | ||||| ||||| || ||||| ||||||||| | || ||||| |||||||||||||| ||||| |||||||| || |
gaatgtttggccatttataacaattgacttcagatatgtagcttaatttta-----tcatctcatttaatcttcctgtaactg-taattaaatctcccttctgcagGTTATTGATTTCCATCAGACTTTAGAAGTAAATGGCATACGATTTTGGTGTTATACAGCTGGCCACGTCCTTGGTGCTGCCATGTTTATGGTTGATATTG
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S23_196V6.1 (Physcomitrella patens), 3'ss of exon 4
tttgtttggtacaattttttttcccagatgcaacacttattt--tgggacggagggacc---tctaaattccagtatatctgctaacagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
|| | || ||| | | | || || | || | || | | | | | | || | | | | | || |||| ||||| |||||||| |||||||| ||||||| ||||| |||||||||||||||||| | ||||||||||| | ||||| || ||||||||||| |||||||
-----atgatgaggttatttactagattattgatatgtacttcctaaaacagcggcatcgtgtttgcaattaagcggttgtataaccctatgttggtgatgacagGTGATTGATTTTCATCAAACTATGGAAGTCAATGGGATTCGATTCTGGTGTTATACAGCAGGCCATGTATTGGGTGCAGCCATGTTCATGGTAGACATAG
upper sequence: GLYMA08G20140.1 (Glycine max), 3'ss of exon 1
lower sequence: PP1S77_275V6.1 (Physcomitrella patens), 3'ss of exon 5
tttgtttggtacaattttttttcccagatgcaacacttattt---tgggacggagggacctctaaattccagtatatctgctaacagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
| |||||| | |||| | | | | ||||| || | | | | |||| ||| | | | | | | || ||| |||||| |||||||| |||||||| ||||||| ||||| ||||| |||||||||||| | ||||||||||| | ||||| ||||||||||||||||| ||||
tgtgtttg-tgttatttactaacatgctagtgtaaactatttgaatgagttgtatcgtactct--atttgggcgattgttaaactatattttcgtgttggcagGTGATTGATTTTCATCAAACCATGGAAGTAAATGGGATTCGGTTCTGGTGTTATACAGCAGGCCATGTATTGGGTGCAGCTATGTTCATGGTTGATATAGMapped EST sequences
Showing partial alignments of ESTs and genomic sequences. See full alignments
ATGC EST sequence
ATGC genomic sequence (exon)
ATGC genomic sequence (truncated intron)
EST:
gi|19453469|gb|BM954879.1|BM954879EST: ATATGCTTTTTGATGAACAGGACATCAATCGCTCCATGGATAAAATTGAG GTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGT
genomic: ATATGCTTTTTGATGAACAGGACATCAATCGCTCCATGGATAAAATTGAGgttccaattt ... gtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGT
EST:
gi|6070136|gb|AW099706.1|AW099706EST: ATATGCTTTTTGATGAACAGGACATCAATCGCTCCATGGATAAAATTGAG GTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGT
genomic: ATATGCTTTTTGATGAACAGGACATCAATCGCTCCATGGATAAAATTGAGgttccaattt ... gtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gacggagggacctctaaattccagtatatctgctaacagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
tgctaac putative branch site (score: 1)
tctaaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtttggtacaattttttttcccagatgcaacacttattttgggacggagggacctctaaattccagtatatctgctaacagaaattagtgactgcagGTTATTGATTTCCATCAAACAGTGGAAGTGAATGGTATTCGATTCTGGTGTTATGCTGCAGGCCATGTCCTTGGTGCTGCTATGTTCATGGTTGACATAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
-ttgtttg
- - - - - - - - - - - - cagatgc
- - - - - - - - - - - - - - - - - - - - - - - - ggaggga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctaac