Sequence
atgc intronic sequence ATGC exonic sequence...tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattatcttatcctggactttgtaaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
Basic information
species | Glycine max |
transcript | GLYMA15G10940.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 4
-----tgaagttggacaatgcttctatgcttc-tgtgtaccttaatgatttattatcttatcctggactttg-taaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
| | || | | ||| ||| || || | | ||| || | ||||| | | | || ||| | || | || |||| |||||||||||||| ||||| |||||||| ||||||||||| ||||| || ||||| |||||||||||||||||||||||||||||||| ||||||||||| |
aagtgtacacatgtattctccttttattttttgcatgggcttctatgtttgtccaa--tatccgaagcaccgatgaacataatgtgtttca-----ttattttgcagTATACACCAGCAATAGATATATGGAGTATTGGCTGCATATTTGCCGAGCTTTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTG
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattatcttatcctggactttgtaaatatatttggtcataaacttttg----tttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
| |||||| | | | || || ||| | | | | || | | | || ||| || | || ||||| |||||||| ||||| ||||||||||| || ||||| ||||| |||||||| || ||||||||||||||||| ||||| ||||| || |||||||| |
----gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaattcttgcagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 3
tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattat--cttatcctggactttgtaaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
| | | | ||||| | | |||| | ||| || | | | | |||| ||| ||| |||| ||| |||||||||||||| ||||| |||||||| ||||| || || ||||| ||||| || || |||||||| |||||||| ||||| ||||| || |||||||| |
catgctcttttgttcataagaagcttcactcttgtataattgccttgtatagtttgttcgatatctgaggaatactgttgaacattgtgtttt--tttacagTATACACCAGCGATAGATATATGGAGTATTGGTTGTATATTTGCGGAACTATTAACTGGAAAACCGCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 4
tgaagttggacaatgcttctatgc---ttctgtgtaccttaatgatttattatcttatcctggactttgt-aaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
|||| | | | | | | ||| || ||| || ||| | | | ||| | | | || | || || | || | |||| |||||||||| || ||||| |||||||| |||||||| || ||||| ||| | || || ||||||||||||||||| ||||| ||||| || |||||||| |
gattgttgcatatttccttctcacctgttccatggccctgtatagtttgtgaaat-atctggagcaccattgaacaaatatgtgttt---tttgttttttgtagTATACACCGGCGATAGATATATGGAGTATTGGCTGTATATTTGCAGAATTGTTAACTGGAAAACCTCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
---------------------------------------tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattatctt-atcctggacttt---gtaaatatatttggtcataaacttttgtttt--tcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
|| || | | | |||| || || || || | | | | || || | | ||| | || || ||| || | | || | || | |||||||||||| || ||||| ||||||||||| || ||||||||||| ||||| || || || |||||||||||||| ||||| ||||| || |||||| | |
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctag---tcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
-tgaagttggacaatgcttctat--gcttctgtgtaccttaatgatttattatcttatcctggactttgtaaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
|| | ||| | || ||| || | | ||| || | || | || || | | | |||| |||| |||||||||||||| ||||| |||||||||||||| ||||| ||||| || ||||| || ||||||||||| || ||||| || ||||||||||| ||| | |
tcatgattcagtgtccatcatattgacaatagttaaccatact--ctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcatttt-cagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
upper sequence: GLYMA15G10940.4 (Glycine max), 3'ss of exon 4
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
---------------tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattatcttatcctggactttgtaaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
| ||| | | | | | ||| || | | | | || | |||| | | || || | ||| |||| |||||||| || || || || || ||||| || ||||| || ||||| ||| | ||||||||||| || ||||||||||||||||||||||||||||| || |
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggtagaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGMapped 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|10238909|gb|BE807805.1|BE807805EST: CAACACGGTGGTATAGGGCTCCTGAGTTGTGTGGATCCTTTTTNTCCAAG TATACACCAGCTATAGACATATGGAGCATTGGCTGCATTGTTGCTGAACTT
genomic: CAACACGGTGGTATAGGGCTCCTGAGTTGTGTGGATCCTTTTTTTCCAAGgtgcaatata ... tgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.attatcttatcctggactttgtaaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
cttttgtttttc CT-rich tract
actttgtaaatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgaagttggacaatgcttctatgcttctgtgtaccttaatgatttattatcttatcctggactttgtaaatatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCTGAACTTTTGACCGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTTCATCAACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA