Sequence
atgc intronic sequence ATGC exonic sequencegtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
Basic information
species | Glycine max |
transcript | GLYMA04G08670.1 |
intron # | 3 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os01g55580.2 (Oryza sativa), 3'ss of exon 3
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtg-atgatacttactgttctgggtttagctgatat-tgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
| | ||||||| ||| ||| | ||||||| || | | ||| | || | |||| |||| |||| | | | || ||| | | | | |||| || | || | || ||||| |||||||| || ||||||||||| ||||| || || |||||||| ||||||||||||||||| |
-----------------------------------cgagtattttttgg-atgccatgtttca------tttttgtacatctcattatctgatttgccctgctatgatgcgtgtacttaatgttagtccctgaaa---ttgccagGAGGCGGCTG-GTGATCTTCCATTAGTTGGGAAGCATAATAAAGGGTGCCACTGCAAGAAGTCAGGTTGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA------
upper sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: LOC_Os02g17460.1 (Oryza sativa), 3'ss of exon 4
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGT-GAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
| ||| | | | | ||| | || ||| | | | || | |||| || | | | || | || | || | ||| | | | || | ||| ||| |||||||||||| || |||||||||| ||| |||| ||| | || ||||| ||||| ||||||||||| |
----------------------------------------aatgtttaggaataatttgttatttcc--ccattaaaatgccaagt-ccattttttttttaccttgagctacatgtg-tttatacagtcttatgtgac-tttcagGATAATTCTGAAGCAATACCTCCGATACCAAAGCACAATAAGGGCTGTCACTGCAGGAAGTCAGAGTGCTTAAAAAAGTACTGTGAATGCTTCCAAGCAA------
upper sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G104246_T01 (Zea mays), 3'ss of exon 3
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
||| | || || | | ||| || | || || | | ||| ||| ||| | | || || || || || ||| || ||| | | | | |||| | || |||| ||||| |||||||| || || |||||||| ||||| ||||| |||||||| ||||||||||||||||| |
-----------------------------------ctatcaaatactgaaattatgtcattattgcatttaatttggacca-agttattgtgctgccatgacatgtggcattaatt--ctagtccatgaaa-----ttgctagGAGGTGTCTA-GTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGCCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA------
upper sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G059678_T01 (Zea mays), 3'ss of exon 3
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
|| || ||||| | ||| || | || | || ||| ||| ||| || | | | || || || || ||| | || ||| | | | |||| | || |||| ||||| |||||||| || || |||||||| ||||| || || |||||||| ||||||||||||||||| |
-------------------------------------atcaattacaggcattatatcattattgcatttcatttcggccatg-ttattgtgctgccttgacacgtcacattaatt--ctagtccat---gaaattttgccagGAGGTGCCTA-GTGATCTCCCTTTAGTAGGGAAGCATAATAAAGGGTGCCATTGCAAGAAGTCAGGATGTCTCAAGAAGTACTGTGAGTGCTTCCAAGCTA------
upper sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: GRMZM2G342588_T01 (Zea mays), 3'ss of exon 3
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgca-tttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
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-----------------------------------------attttatgtttgatttactt---ctatttgattcagttgaaatatttctttatatgtttcatatattgtttagctaatcttagcaacttgaaccggctatcagGATGCTGGAGCACTACCTTCACATCC----AAAGCATAATAAAGGTTGTCACTGCAAGAAGTCAGGTTGTCTAAAGAAATACTGTGAATGTTTTCAAGCGAATA---
upper sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: Vv04s0008g03670.t01 (Vitis vinifera), 3'ss of exon 4
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttgg-catgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
|||||||||| | | ||| | | || |||| ||| ||| | | | | |||| | || | | || | || || | | | | | ||| | || | | | | |||||||||||||||||||| ||||||||||||||||| ||||| |||||||| ||||||||||| ||||| |
-----------------------------aatgtgttatttccctaaagatgtgaaattatcaa------ttttcatga--atattgataact---gatttactt----ttctttctgggctgaactgttcaaaa-cgaatctagGAAGAGGCTGGGAAAGTCCCATTGGTGGGAAAGCACAATAAAGGATGCCACTGCAAGAAATCAGGTTGCCTCAAGAAGTACTGTGAGTGCTTTCAAGCAA------
upper sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S10_254V6.2 (Physcomitrella patens), 3'ss of exon 5
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
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----------------------------tcatgtatt----ttctgtagtaccaaggtgtt---ccttttttatg-gacatttcccctcaatctgggtc-agtggatttcggaactaata---gaactttattattgcagGAGGATGCTGGA----GAGCATCCATTGGCGGGTAAACACAACAAAGGATGTCATTGCAAGAAATCCGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCTA------
upper sequence: GLYMA04G08670.1 (Glycine max), 3'ss of exon 3
lower sequence: PP1S9_436V6.1 (Physcomitrella patens), 3'ss of exon 5
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
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-------------------------------cgtattcct--tctgttgtaccaaa-ttatattccatagtttc---attatttttcttaacctgggcg-agtggttgacgaaactga--tggcatcttggttattgcagGAGGATGTTGGAGAGCATCCTC----TGGCGGGCAAGCACAACAAAGGATGCCACTGTAAAAAGTCGGGGTGCCTCAAGAAGTATTGCGAATGCTTCCAAGCCA------Mapped 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|208060019|gb|GD857447.1|GD857447EST: CTTTCAGACCAAAAATTGCTAGCAGTCCACAAGAACAAAGAGATTCCAAG GAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAG
genomic: CTTTCAGACCAAAAATTGCTAGCAGTCCACAAGAACAAAGAGATTCCAAGgtttgtagtt ... ttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
agttaac putative branch site (score: 3)
tcttgttt putative PPT
atttaaatatcttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtttgtagttcaatttcaactccctcaaacatgtgttattggtttttggcatgaggcttttaagccaagtttttgtgatgatacttactgttctgggtttagctgatattgtagttaacttgtgcatttaaatatcttgtttgaacacagGAATGTGAAATTAAAGTAATAGGAAAGCACAATAAAGGATGTCACTGCAAGAAATCAGGCTGCCTTAAGAAGTATTGTGAGTGCTTCCAAGCCAATATCC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT