Sequence
atgc intronic sequence ATGC exonic sequence...tggacaatgtttctatgcttctgtgtaccataatgatttattatcttatcccggacctggacttggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
Basic information
species | Glycine max |
transcript | GLYMA13G28120.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os05g05160.1 (Oryza sativa), 3'ss of exon 4
---tggacaatgtttctatgcttctgtgtaccataatgatttattatcttatcccggacctggact--tggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
|| ||| | | | ||| | | | | | || | || ||| | | | | | | |||||| | || | || |||| |||||||||||||| ||||| |||||||| ||||||||||| ||||| || ||||| || ||||||||||||||||||||||||||||| || |||||||| |
aagtgtacacatgtattctccttttattttttgcatgggcttctatgtttgtccaatatccgaagcaccgatgaacataatgtgtttca-----ttattttgcagTATACACCAGCAATAGATATATGGAGTATTGGCTGCATATTTGCCGAGCTTTTAACCGGAAAACCTCTTTTCCCTGGGAAGAATGTGGTTCATCAACTTG
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os11g17080.1 (Oryza sativa), 3'ss of exon 4
--tggacaatgtttctatgcttctgtgtaccataatgatttattatct-tatcccggacctggact--tggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
|||| | | | | || || ||| | | | || |||||| | ||| ||| | | ||| | ||| ||||| |||||||| ||||| ||||||||||| || ||||| |||||||||||||| || ||||||||||||||||| ||||| ||||| || |||||||| |
gcaatgaaatgctgtctagttccagttgctggctatatttttctttgtacatataatgcctggagtatcggtgaaccttatactgttcaaattcttg-----cagTACACACCAGCAATAGATATATGGAGCATCGGTTGCATATTTGCAGAACTTTTAACAGGAAAACCTCTTTTCCCCGGGAAAAATGTGGTGCATCAACTTG
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G089484_T01 (Zea mays), 3'ss of exon 4
---tggacaatgtttctatgcttctgtgtaccataatgatttattatcttatcccggacctggac--ttggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
|| || |||| | || ||| |||| | ||| | || | | ||||| | |||| || || | || | |||| |||||||||| || ||||| |||||||| |||||||| || ||||||||| | || || ||||||||||||||||| ||||| ||||| || |||||||| |
gattgttgcatatttcctt-ctcacctgttccatggccctgtatagt-ttgtgaaatatctggagcaccattgaacaaatatgtgttt---tttgttttttgtagTATACACCGGCGATAGATATATGGAGTATTGGCTGTATATTTGCAGAATTGTTAACTGGAAAACCTCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G017351_T01 (Zea mays), 3'ss of exon 3
tggacaatgtttctatgcttctgtgtaccataa----tgatttattatcttatcccg---gacctggacttggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
||| | | || | | | | | | | || | ||| ||| | | | | | || || | ||| ||| |||| ||| |||||||||||||| ||||| |||||||| ||||| || || ||||| ||||| || || |||||||| |||||||| ||||| ||||| || |||||||| |
-----catgctcttttgttcataagaagcttcactcttgtataattgccttgtatagtttgttcgatatctgaggaatactgttgaacattgtgtttt--tttacagTATACACCAGCGATAGATATATGGAGTATTGGTTGTATATTTGCGGAACTATTAACTGGAAAACCGCTTTTCCCGGGGAAAAATGTGGTACATCAACTTG
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
lower sequence: AT5G19010.1 (Arabidopsis thaliana), 3'ss of exon 4
----------------------------------tggacaatgtttctat---gcttctgtgtaccataatgatttattatcttatcccggacctggacttg---gtaaacatatttggtcataaacttttgtttt--tcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
|| | ||| || | ||| | | | | | ||| || | | | | || | ||||| ||| || | | || | || | |||||||||||| || ||||| ||||||||||| || ||||||||||||||||| || || || |||||||||||||| ||||| ||||| ||||||||| | |
gtgaccatgattttgtatatatactttcatcgaatgtttcaaattttcatagggaatctagtcagtagacactatagctctctcattcagattataaaattttatggtaacattttttttctttatctatgcttctgttcagTATACACCGGCAATAGATATATGGAGCATCGGGTGCATTTTTGCAGAACTCTTAACAGGGAAACCTCTTTTCCCCGGGAAAAATGTGGTCCATCAATTGG
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv05s0020g02530.t01 (Vitis vinifera), 3'ss of exon 4
tggacaatgtttctatgc---ttctgtgtaccataatgatttattatcttatcccgg-acctg-gacttggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
||| ||| || | | | || ||| | | || ||| | ||||| || || ||| || | | | |||| |||| |||||||||||||| ||||| |||||||||||||| ||||| |||||||| ||||| || ||||||||||| || ||||| || |||||||| || ||| | |
----tcatgattcagtgtccatcatattgacaatagttaaccatactctaggtatgatacctgtgatctgactgtcattttcgtttttgctctttcatttt-cagTATACACCAGCAATAGATATATGGAGCATTGGATGCATCTTTGCAGAGCTTTTAACTGGAAAACCTCTCTTTCCTGGAAAAAATGTTGTTCACCAATTGG
upper sequence: GLYMA13G28120.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S87_157V6.2 (Physcomitrella patens), 3'ss of exon 4
----------tggacaatgtttctatgcttct-gtgtaccataatg--atttattatcttatcccggacctggacttggt---aaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
|| | | ||| || | ||| ||||| | | ||||| | | | | || || | || | | | || || | ||| |||| |||||||| || || || || || ||||| || ||||| || ||||| ||| | ||||| ||||| || ||||||||||||||||||||||| ||||| || |
gtaacactagtgcgctctcgttcagtggaggtcgtggaccatgacacaagttattgggt-agaacatatttgtgagtgattttgaataagtgttgttatgtcccttttttttacagTATACTCCTGCGATCGATATCTGGAGTATAGGCTGTATATTTGCGGAAGTGTTGACCGGAAAGCCACTTTTCCCTGGGAAGAATGTTGTTCATCAGCTGGMapped 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|11413042|gb|BF425062.1|BF425062EST: CAACCAGGTGGTATAGGGCTCCTGAGTTGTGTGGATCCNNNNNNNCCAAG TATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTT
genomic: CAACCAGGTGGTATAGGGCTCCTGAGTTGTGTGGATCCTTTTTTTCCAAGgtgcaatata ... tgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcccggacctggacttggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
cttttgtttttc CT-rich tract
ataaacttttgttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tggacaatgtttctatgcttctgtgtaccataatgatttattatcttatcccggacctggacttggtaaacatatttggtcataaacttttgtttttcagTATACACCAGCTATAGACATATGGAGCATTGGCTGCATTTTTGCAGAACTTTTGACGGGAAAACCTCTTTTCCCTGGGAAGAATGTTGTCCATCAACTAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - caatgtt
- - - - - - ctatgct
- - - - - - - - - - -tgtgtac
- - - - - - - - - - - - - - - - - - - - - - - - - - - -cctggac