Sequence
atgc intronic sequence ATGC exonic sequencegtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
Basic information
species | Glycine max |
transcript | GLYMA17G34690.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os06g40940.3 (Oryza sativa), 3'ss of exon 4
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatca-gGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
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-------------------------------------gtgaggggaattca-gcat-----ttgtttagtttct--aaatgcaaactgttcatcagatgatctg-----aaatggcttgttttgtgatgaagGAAATGTTTGATGACTTGGGCGATCTGCTGTGCAAGATCACTGGCTTTGATTCTTTCTCTTTGCAACCAAATGCTGGTGCTTCAGGGGAGTATGCCGGAT
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g51410.1 (Oryza sativa), 3'ss of exon 5
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatca-gGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
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--------------------------------------gtgagggaattcac-catttatttagtttctaaatgcaaactgttcatcagatgatctg------------aaatggcttgttttgtcatgaagGAAATGTTTGATGACTTGGGCGATCTGCTGTGCAAGATCACTGGCTTTGATTCTTTCTCTTTGCAACCAAATGCTGGTGCATCAGGGGAGTATGCCGGAT
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G104310_T03 (Zea mays), 3'ss of exon 5
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
|| | |||| ||| || || || | | | | | | ||| | | | | | | | ||| | |||| || |||||||||| | | ||||| | ||||| ||||| ||||| || ||||| || ||||| ||||||||||||||||||||||| ||||| ||||| |||
------------------------gtaaggaccatgattcag-----tttctatcctaatgccaaagtattc---acagcatgaatttgcaaacat------ctggaataacttgttt--tctgtcat-agGAAATGTTTGACGACTTGGGCAACCTGTTATGCACGATCACAGGTTTTGATTCTTTCTCTTTGCAACCAAATGCTGGTGCTGCAGGAGAGTATGCTGGAT
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT2G26080.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
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------------------------------------------gtgaggccacatatttgat---ttacctgactagaaatttaact---acgtactgaattttttgtttgacaactta----------tagGAAATGTTTACGAATTTGGGTGAGCTCTTATGTACGATCACTGGATTCGACTCTTTCTCATTGCAACCTAATGCCGGTGCTGCTGGCGAGTACGCCGGGC
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G33010.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
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-------------------------------------gttagtgactttcttg-attcat-ctgaggtctgatttagaaagttgaacaatgaac-tgatatctt-gtcca------catgtatg----tagGAAATGTTCGAAAATTTGGGTGACCTCTTGTGTACGATCACTGGGTTTGACTCTTTCTCGTTGCAACCTAATGCTGGTGCTGCTGGTGAGTATGCCGGGC
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv11s0016g02280.t01 (Vitis vinifera), 3'ss of exon 6
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
|| | | | ||||||| || | |||| | | || || ||| || ||| | |||| ||| | | | |||| ||||||||| ||||||||||||| ||||| ||||||||||| || ||||| ||||| ||||||| |||||||||||||| || || ||||| || |
---------------------------gtaacttaaatttcttgaaattctgat-tctatatccacatataagagtaatccaaggtcagacttcacccattcact-cataaattttca----ttttcttagGAGATGTTCAATGATTTGGGTGAACTATTGTGTACCATCACTGGATTCGACTCGTTCTCTCTGCAACCTAATGCTGGTGCTGCAGGGGAGTATGCTGGGC
upper sequence: GLYMA17G34690.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv04s0008g01300.t01 (Vitis vinifera), 3'ss of exon 5
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
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----------------gtagt--taccaacattttctttacctggaagttacatgtttgtgctgt--ctttcttgcattaactagc--aaattgacattgtttgctgttgaattatgattttttttgctagGAAATGTTCAATAACTTGGGTGAACTATTATGTACCATCACTGGATTTGACTCTTTCTCATTGCAACCCAATGCTGGTGCTTCTGGCGAGTATGCTGGCCMapped 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|17519697|gb|BM188739.1|BM188739EST: TTACTGATATTCACCCTTTTGCACCAGTTGACCAGGCTCAAGGTTATCAG GAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGAC
genomic: TTACTGATATTCACCCTTTTGCACCAGTTGACCAGGCTCAAGGTTATCAGgtaattctat ... ctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGAC
EST:
gi|209728382|gb|BW652039.1|BW652039EST: TTACTGATATTCACCCTTTTGCACCAGTTGACCAGGCTCAAGGTTATCAG GAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGAC
genomic: TTACTGATATTCACCCTTTTGCACCAGTTGACCAGGCTCAAGGTTATCAGgtaattctat ... ctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
gtctaaa putative branch site (score: 3)
ttttcttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattctatgtttaaataatcttacaacaattatgactcaaagaaattcacatatatatactgttgcgtgcctgaaaatatgggatagaagtcgtgttttctttgtctaaacaatcaaatctggtatcagGAAATGTTCAATAATTTGGGTGAACTGTTGTGCACCATCACTGGGTTTGACTCCTTCTCCTTGCAACCAAATGCTGGTGCTGCTGGAGAATATGCCGGAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA