Sequence
atgc intronic sequence ATGC exonic sequencegtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
Basic information
species | Glycine max |
transcript | GLYMA06G47300.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os01g17010.1 (Oryza sativa), 3'ss of exon 4
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
| | |||||| ||| || | | ||| | || || | | |||||||| | ||| ||| || | | || || | || | ||||||| |||||||| |||||||||||||||||||||||||| |||||||||||||| |||||||| ||||| |||||||||||||| |||||||| |||||
---------------------gtattattccctcctg---gttctgctattatggcatataata------ttctgtgagaaccaatttatgtac----atgtgatatatgcta--attaatcttttgttgttcagGTGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGTGTTGGCATCAGTGGTCAAGAAGGACGGCAGGCTGTAATGGCATCAGATTTTGCGATGGG
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g20949.1 (Oryza sativa), 3'ss of exon 4
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
| ||||| | ||||||| || | || | || | | | ||| || | | | || || | || ||||||| |||||||| || ||||||||||||||||||||||| |||||||||||||||||||||| |||||||||| |||||||| ||
-----------------------------------gtacagtttttttttctcgccaaatattcaggaattact---tgatttactatatttttctcaatctgaaaag-------------agGTACCTTTCCAGGTGCAAATGATGTATCCATGATTCAAATGGCTGATGTTGGTATTGGCATCAGTGGACAAGAAGGAAGGCAAGCTGTTATGGCATCAGA------------
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G840699_T01 (Zea mays), 3'ss of exon 4
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
| | |||||| | | || | | |||| | | || | || ||||| | || |||| | ||| | ||| |||| || |||||||| |||||||||||||||||||||||||| ||||||||||||| |||||||| || |||||||| |||||||| |||||| | |||||
---------------------gtattattccctcctgcttctcttattatggtgtattttattc-----tctatgatcttgatatgttcaaatctgatat---atgaatttccttaccttggcgtt------cagGCGCAAATGATGTTTCAATGATTCAAATGGCTGATGTTGGGATTGGCATCAGTGGCCAAGAAGGTCGACAAGCTGTTATGGCATCAGATTTTTCTATGGG
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G407825_T01 (Zea mays), 3'ss of exon 4
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
| ||||| | |||| | | ||| ||| | |||| || | | || ||||| ||| || || |||| | | | ||| | ||||||| |||||||| || ||||||||||||||||| ||||| | ||||||||||| ||||| || |||||||||| ||||| || |||||||| |||||
-----------------------attattccaacttaaaatgtagg--acaaaggaagtagctcagaacttcata-----tatgttttatcttcacgagt-caaaaaatatgaaaacatacacgtt----ttcagGTGCAAATGATGTATCCATGATTCAAATGGCTGACGTTGGCATCGGCATCAGTGGGCAAGAGGGAAGGCAAGCTGTTATGGCCTCAGATTTTGCCATGGG
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: AT5G04930.1 (Arabidopsis thaliana), 3'ss of exon 4
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
|| || | | | | | ||||| | | || || | | | | | | | | ||| | || | | ||| ||||| | ||| | |||||||| ||||||||||| ||||||||||||||||||||||| || || || || ||||||||||| || |||||||| |||||||||||||| ||||||||
-------------gtaatgaccccactcttctttccaaaaagtagtctgc--ctgatcctgtctaaacagacccagttctttggttttttatttt---------catcttctcatatgc-tttgtgttttgacagGTGCCAATGATGTCTCCATGATTCAAATGGCTGATGTTGGGGTAGGGATAAGCGGACAAGAAGGTCGCCAAGCTGTGATGGCATCTGATTTCGCAATGGG
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv13s0047g01210.t01 (Vitis vinifera), 3'ss of exon 4
gtaattgagttttgttataccttgtcattccccttcaaaagttt--gatagcaataga--aaatattgagaagtttttgg----ctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
||||| || || | || | ||| | | || | | || ||| ||| | | ||||| ||| |||| | | || | | ||| ||| || | | | || | | | |||||||||||||||| |||||||| |||||||||||||| ||| |||| |||||||| ||||| ||||| |||||||| |||||||| ||||||||||||||
----gtgagtattattcttccaatttatttaagactgataacttatgcttgcccaagaccaaaaaattagaagggaaaaaaaatctgatctgttgtttggttttaggc-taacgc-ttgaaatttctattggatgattcccagGTGCTAATGATGTTTCAATGATACAAATGGCTGATGTGGGAATTGGTATCAGTGGCCAAGAGGGCCGTCAAGCTGTCATGGCATCAGATTTTGCAATGGG
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S38_368V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaattgagttttgttataccttgtcattccccttcaaaagtttgata-gcaatagaaaatattgagaagtttttggctggtctgatttatgttctga-ggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
|| ||| || | ||||| | | || || | |||| | | || |||||| ||||| ||| || || | | || ||||||| || || ||||| ||||| |||||||| || || ||||| ||||||||||| || ||||| |||| ||||| ||||| |||||||| ||||| ||
----------------------------------ataagtgttgaatctgtcttagaaggtgat-agcagcagcta-ctggcatcaagtacgttctggtagtgtagatcatttaat-gtgtcgtttctttatcgcagGTGCAAACGACGTCTCGATGATACAAATGGCCGACGTCGGAGTGGGCATCAGTGGGCAGGAAGGGAGGCAGGCTGTCATGGCCTCTGATTTCGCAATTGG
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: PP1S39_64V6.1 (Physcomitrella patens), 3'ss of exon 6
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatg---tgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
||| || ||| || || | || || || | ||| | | ||| | || || | | ||| ||| || | || || | |||| || || || || |||||||| ||||||||||||||||||||||||||||| || || ||||| || ||||| || ||||| |||||||||||||||||
---------------------------------ttcgtg---ttactagtaagttgaagctcttcaaaacttcaggttc-tcttacatgtgtctttag-tgcactttattacatgtcacaaggcttgctattgttcagGGGCAAACGACGTGTCAATGATACAAATGGCTGATGTTGGAGTTGGCATCAGCGGGCAGGAAGGGCGACAAGCAGTTATGGCGTCTGATTTTGCAATGGG
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ23939 (Selaginella moellendorffii), 3'ss of exon 5
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccat-tatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
| || ||| | || ||| | | | ||| | | | | ||| | |||||| ||||| || | |||||||| ||||| || || || ||||| || || |||||||||||||||||||| || |||||||| ||||||||||||
----------------------------------------------------------------------------gtaatcatctttgt-ttaggagatctcttgaataatttctctttaatctttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCC
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ16263 (Selaginella moellendorffii), 3'ss of exon 6
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgtt-ctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
|||| ||||| | ||| || ||| | || || | || |||| | | ||| | |||| || ||||||||||| ||||| || | || ||||||||| |||| | ||||| || ||||| |||||||| || ||||||||||| |||||| ||||
-------------------------------------------------------------gtgagtgattttttttctttttgacttttgtggcctagaagtggt---tttcatt-tcccgaagttgtgct-cagGAGCCAATGATGTCTCCATGATACAGACAGCAGATGTTGGAATTGGATTGAGTGGCCAGGAAGGTCGGCAAGCAGTCATGGCATCTGACTTTGCATTGGG
upper sequence: GLYMA06G47300.1 (Glycine max), 3'ss of exon 5
lower sequence: EFJ21562 (Selaginella moellendorffii), 3'ss of exon 5
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
| | |||| | | || ||||| ||| || | ||| | |||||| ||||| || | |||||||| ||||| || || || ||||| || || |||||||||||||||||||| || |||||||| ||||||||||||
------------------------------------------------------------------------gtaatcatctttgtttaggagttctcttg-aataatttctctttaatct---ttaatctttagGTGCGAATGACGTAGCCATGATTCAGATGGCGGACGTAGGCGTTGGTATAAGCGGACAAGAAGGCCGGCAAGCAGTGATGGCATCGGATTTTGCAATGCCMapped 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|254342204|gb|GR853341.1|GR853341EST: TGCCCTTGTGAAGAATAGAACATCTGACATGACACTAGCCATTGGAGATG GTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCA
genomic: TGCCCTTGTGAAGAATAGAACATCTGACATGACACTAGCCATTGGAGATGgtaattgagt ... tacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
gtctgat putative branch site (score: 4)
taataaattccattat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaattgagttttgttataccttgtcattccccttcaaaagtttgatagcaatagaaaatattgagaagtttttggctggtctgatttatgttctgaggtgtaataaattccattatgcatgtgttacattacagGTGCTAATGATGTCTCAATGATTCAAATGGCTGATGTTGGAGTTGGCATCAGTGGACAAGAAGGCCGGCAAGCTGTAATGGCATCTGATTTTGCAATGGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG