Sequence
atgc intronic sequence ATGC exonic sequencegtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgattttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
Basic information
species | Glycine max |
transcript | GLYMA03G00670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g17180.1 (Oryza sativa), 3'ss of exon 5
gtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgattttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
|| | | |||| | | |||| | | | | | || | || | ||| | | | | || ||| | | || || ||||| ||||||| || ||||||||||||||||| ||||||||| | ||||| || |||||||| || |||||||| || || ||||| || || |||||||
-----------------------gtgcttatacaagtttctctagtcaatt-ggttttctttacatattctg-cagtcatta-ctctaattattttgctcgtaac-ttcttcctgtagATACTGAAGGAGCTGCATAAATCTTGTCAAAGAGAAGATGGTTCTGATGATCAGAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAGATCCAAA
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G079196_T01 (Zea mays), 3'ss of exon 5
gtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgattttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
| | | | || | | || | | || || || || ||| | ||| | | | || || || ||||||||||||||||| ||||||||||| ||||||||||||||| | ||||| || |||||||| || |||||||| || || ||||| || ||||| ||||
------------------------------------gtccttggatcatttc---tttcatagtctttgatgcaataaatttgc-ttgtattattaaattacattctt--actggcagATATTGAAGGAACTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAACTTTTGGAAGTCTATGCTATTGAAATACAAA
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G132804_T01 (Zea mays), 3'ss of exon 5
gtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgattttg--ttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
|| | | | || || | | || | | | | | || ||| || ||||| | || | | || |||||||||||||| || ||||||||||| ||||||||||||||| | ||||| || |||||||| || || ||||| || || ||||| || ||||||||||
------------------------------------gttcttggatcactt---atttagttatagtcttcgatg-cagtaagt-ttgtctatattattaaattagattcttactggcagATATTGAAGGAGCTGCATAAATCTTGCCAAAGGGAAGATGGTTCTGATGATCAAAAGAAAGGCACACAGCTTTTGGAAGTCTATGCTATTGAAATCCAAA
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv08s0040g00430.t01 (Vitis vinifera), 3'ss of exon 5
gtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatc-catgagcgttgagtaatttattgattttgttgaaccct---cagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
||| | |||| | | || |||| | |||| ||| || |||| | ||| ||| ||| ||| | ||||| || |||||| || || || ||||| ||||| |||||||| |||||||||| ||| ||||||||||||||||| || |||||||||||||||||||| || || |||||||| || || ||||
gtatttttttagccctgtttggtcagatg----acgcattcctgctctgttctcatgtgcccttatatatatgtaaaacattttattatggtaatctaaggatttt--tggacactgaacagATTTTGAAAGAACTTCACAAATCTTGTCGAAGAGAAGATGGTACAGATGATCAAAAGAAAGGAACCCAACTTTTGGAAGTATATGCAATTGAGATTCAAA
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S105_216V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgatt--ttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
| | || || | | || ||| | || ||| || || || | || | || ||| | | | ||| | || | | |||| |||||||| ||||| ||||||||||||| ||||||||| ||||||||||| ||||| || || || || | || |||||||| || ||||| || |
-------------actccttggtat-acatcagt-gttatgtagaataacttttatagttgcac-tgcatcg----tcagtagcatcatatgtgatgctgaccaatggtcgtgtgtttagATCTTGAAGGAGCTTCACAAATCTTGTCAAAAGGAAGATGGCACAGATGACCAGAAGAAGGGCACGCAGCTGCTGGAAGTTTATGCGATTGAAATTCAGA
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S124_47V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------gtaacatattagtattttgtgcaat---gatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgattttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
|| || | |||| || | | || || ||||| | | | ||||| | | | | || | | ||| | | | | | |||| | || ||||| |||||||| || |||||||||||||| | ||||||||||||||||||||| ||||| || || ||| | | ||||| ||||| ||||| || || |
gtaagtattctgcccgttgactcctcaactttattttcatatctttcaactttatctagtattgaatgatttcgtttactcggaataccagtacttttcaaaatgggatgtaatgtgtagtaaattccttgttctgagaaaacttgtgatactcacag--cttgtcgtacgtgcagATTTTGAAGGAGCTCCATAAATCTTGTCAGAAGGAAGATGGTACAGATGACCAGAAGAAGGGCACACAATTGCTGGAGGTGTATGCGATAGAGATTCAGA
upper sequence: GLYMA03G00670.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S90_192V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------gtaacatattagta--ttttgtgcaatgatgttggttgttttccagcttaatttgaatgttt-ctgtatctattggtatccatgagcgt-tgagtaatttattgattttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
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gtaagttcgctgccagttgatttctccacaatatcttcatatgtcctattttatctgataataaatgtcagtcgcttatctcaat-gcttttcagttcgagatatatgttcgcagaatatatt--ttttcgtacacaaatgtgagatgcttctaatttcttagaactgcagATTTTGAAGGAGCTCCACAAATCTTGTCAGAAAGAAGATGGTACAGATGATCAGAAGAAGGGCACACAATTGCTCGAGGTTTATGCGATAGAGATTCAGAMapped 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|151398925|gb|EV268796.1|EV268796EST: AGCTTTGTAAGATCTTCTTTGACATTGGGGAATATGGACGGATGAGTAAG ATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGAC
genomic: AGCTTTGTAAGATCTTCTTTGACATTGGGGAATATGGACGGATGAGTAAGgtaacatatt ... gaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tatctattggtatccatgagcgttgagtaatttattgattttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
tattgat putative branch site (score: 3)
ccctc putative PPT
taatttattgattttg 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaacatattagtattttgtgcaatgatgttggttgttttccagcttaatttgaatgtttctgtatctattggtatccatgagcgttgagtaatttattgattttgttgaaccctcagATATTGAAGGAACTTCATAAATCTTGTCAAAGGGAAGATGGTACAGATGACCATAAGAAAGGAACCCAACTTTTAGAGGTTTATGCAATAGAAATCCAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA