Sequence
atgc intronic sequence ATGC exonic sequencegtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcatttccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
Basic information
species | Glycine max |
transcript | GLYMA13G07650.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os05g27940.1 (Oryza sativa), 3'ss of exon 5
---gtgagcttt--tgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcattt-ccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
| |||| | | || | || | || | | |||| | ||| | | || | | | | | |||| | | || | | | || | ||| ||||||| ||||||||||||||||| ||||||||||| || ||||| || || || | ||| ||| || || || || || || |
taccttagctgtatttcaaacataatcacgggcgcta-atgatttttatgctgt--ctcgctgaattcaaacaacgctgaccttgtatgaacttgt-gctgcagATCTTCCTGGACCCAAAGGAGCGCAACAACACCGAGTACAAGCTCGACACTTTCAGCTCTGTCTACAGGAGGCTCTGTGGGAAGGACGTCGTGTTCGACT
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g18580.1 (Oryza sativa), 3'ss of exon 4
--------gtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcatttccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
|| |||| ||| | | | | | | ||| |||| | | | | | | | ||| | | | |||| | || || ||||||||||||| |||||||||||||| || || |||||||| ||||| || || | ||| || | | |||| ||| |||||||| | || ||||
catgtacaatgggcttgctgtaagcctgtaactaatccagcagcatgacatttctgtttgctaggttagtattgacccatgtg----tattgatgtgtt--ttcagATTTTCTTGGACCCAAAGGAGCGCAACAATACCGAATACAAGCTTGAGACCTTCTCCGCAGTCTACCGCAGGCTTTGTGGGAAAGATGTTGCCTTCGAGT
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g18570.1 (Oryza sativa), 3'ss of exon 5
--------gtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcatttccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
|| |||| | ||| | | | | | || |||| | | | | | | | ||| | ||| |||| | || || ||||||||||||| |||||||||||||| || || |||||||| ||||| || || | || || | | |||| ||| |||||||| | |||||||
catgtacaatgggcttgttgtaagcctgtaactaatcctgcagcatgacacttctgtttgctaggttagtattgacccatgtgtttt----gatgtgtt--ttcagATTTTCTTGGACCCAAAGGAGCGCAACAATACCGAATACAAGCTCGAGACCTTCTCCGCGGTCTACCGCAGGCTTTGTGGGAAAGATGTTGCCTTTGAGT
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G030016_T01 (Zea mays), 3'ss of exon 5
---gtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcattt--ccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
| || || || | | || | ||| | | | || ||| |||||| | | || | || |||| | | | || || || ||||||||||||| |||||| | ||||||||||| |||||||||||||| | ||| || || | | ||| ||| |||||||| || |||||||
tgccttggcattagttacctaga-atttctttatacatttatggtttgttggctaacatatagca-gcaagttacttaaccttctcttgtaatgcca-ttcagATTTTCTTGGACCCAAAGGAGAGGAACAACACTGAATACAAGCTGGAGACCTGCACTGCGGTCTACCGCAGGCTGTGTGGGAAAGATGTGGTCTTTGAGT
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G085420_T01 (Zea mays), 3'ss of exon 6
--gtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataac-ttgtaaagcattt--ccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
| ||||||| | | || || | || || || | ||| | | | || | | || | || |||||| | | ||| || || ||||||||||||| |||||| | |||||||| || |||||||||||||| | ||| ||| || | | ||| ||| ||||||||
gccttgacttttgttacctaga--attgcttggatacatttatggtttcatggctaacatcatgcagcaagttacttaaccttttcttgtaatgtca-ttcagATTTTCTTGGACCCAAAGGAGAGGAACAACACCGAATACAAGCTGGAGACCTGCACTGCAGTCTACCGCAGGCTGTGTGGGAAAGATGTG----------
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: AT1G48830.2 (Arabidopsis thaliana), 3'ss of exon 5
gtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcatttcctt--ttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
|| | | | | || | || | | | || ||| || | || | | | | ||| | | ||||| ||||||||||| ||||| | |||||||| ||||||||| | ||| |||| |||| ||||| | ||||| ||||| |||||||| || |||||||
---------------gtaagtcaaaattcgaagattattaccatacaggaag--atgtaattttttgtttatctaataaatgggatttgtgtggttgaagGTCTTCTTGGACCCAAAGGAAAGGAACAACACAGAGTACAAGGTTGAGGCTTTCTCTGCGGTTTACAAGAAGCTCACTGGCAAAGATGTCGTCTTTGAGT
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: EDO96962 (Chlamydomonas reinhardtii), 3'ss of exon 4
--gtgagcttttgtgaagttgatgataggttaaatgtcctt-ttctttttgttccccatataacttgtaaagcatttccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
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gattgcgctctttgttgtgtgtcgcggtgatcgccgtctgtgctgcacccgtgcccgacccccccccccccgccactgctgcaacacgtgcgctg-ttcagGTGCACCTGGACCCCAAGGACCGCAACTCCACCGAGTACAAGCTGGAGACCTTCGGCAGCGTGTACAAGCGCCTCACAG---------------------
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: EFJ26379 (Selaginella moellendorffii), 3'ss of exon 4
gtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcatttccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
|| | ||| || || ||| | | | | || ||| || | | | |||| | | | ||||||||||| ||||||| ||| ||||||||| ||||||| | || || || || | ||||| ||||| || ||||| | ||||||||
----------------------gtaaga-aaactccccttcatttccggcgctctagtgac-----gagc-----------tcgaaacgtttttgcagGTCTACCTTGACCCCAAGGAACGCAACAGCACCGAGTACAAGTTGGAGACGTACTCGGGTGTCTACAAGAAGCTGACTGGCAAGGATGTGGCATTTGAGT
upper sequence: GLYMA13G07650.2 (Glycine max), 3'ss of exon 6
lower sequence: EFJ14715 (Selaginella moellendorffii), 3'ss of exon 4
gtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcatttccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
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--------------------------gtaagaaaac---tccccttcatttccggcgtt-ctagtgacgagct---------cgaaacgtttttgcagGTCTACCTTGACCCCAAGGAACGCAACAGCACCGAGTACAAGTTGGAGACGTACTCGGGTGTCTACAAGAAACTGACTGGCAAGGATGTGGCATTTGAGTMapped 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|58023795|gb|CX710536.1|CX710536EST: TTGTTGGCAAACGGGTCAGATATAGAATTGATGGCTCAAAAATAATGAAG GTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACT
genomic: TTGTTGGCAAACGGGTCAGATATAGAATTGATGGCTCAAAAATAATGAAGgtgagctttt ... atcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACT
EST:
gi|209701687|gb|BW667391.1|BW667391EST: TTGTTGGCAAACGGGTCAGATATAGAATCGATGGCTCAAAAATAATGAAG GTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACT
genomic: TTGTTGGCAAACGGGTCAGATATAGAATTGATGGCTCAAAAATAATGAAGgtgagctttt ... atcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttttgttccccatataacttgtaaagcatttccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
atataac putative branch site (score: 3)
atataacttgtaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagcttttgtgaagttgatgataggttaaatgtccttttctttttgttccccatataacttgtaaagcatttccttttgtcaatgtatcaattaagGTTTTCTTGGACCCCAAGGAGCGCAACAACACTGAGTACAAGCTGGAGACTTTTTCTGGAGTTTATAGAAAGCTTACTGGAAAAGATGTAGTATTTGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG