Sequence
atgc intronic sequence ATGC exonic sequence...ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
Basic information
species | Glycine max |
transcript | GLYMA13G18670.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os10g33640.1 (Oryza sativa), 3'ss of exon 5
--------------------------ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgt-----tctacatctttttg---tgtgtgtttgtaatttttgaatgt--ataaatg-ttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
|||||| | || | | | | || | || | | | | ||| || || | | |||| | |||||| || | |||| || ||||| || ||||| || |||||||| || || |||||||||||||||||| | || || |||||||| ||||| ||||||||
gttagtagctagcaaatgtgccaacaatcattagaaacttcttcagaattcacctgttattccttgtgtcattatctatttctcaatgcattcagaattttcgtttccatgttttgactggcagttaatgatttcagGCATACTCCACTGTCGGTACACCGGACTACATTGCTCCAGAAGTTCTTCTAAAAAAGGGTTATGGAATGGAGTGTGATTG
upper sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G088245_T01 (Zea mays), 3'ss of exon 5
ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
| ||| || | || || | | ||| | | || | ||| | | ||| | ||||||||| || || || || |||||||| || || ||||||||||||||| |||||||||| || |||||||||||||| ||
--------------gtcagtaatcatttttttaccacttgatgactcgatctc--ttgatatgcaaatctttttgacaagtgatcattctggctgcgcagGCTTACTCGACCGTCGGAACACCAGACTACATCGCTCCAGAAGTTCTTCTGAAGAAAGGCTACGGGATGGAATGTGACTG
upper sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
lower sequence: Vv07s0005g03690.t01 (Vitis vinifera), 3'ss of exon 5
-----ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
|| | | | | | | | | | || | || | || ||| | | | | | |||||| || || | || |||||||||||||| || ||||| |||||||| ||||| |||||||||||| | ||||||||||||||||||||||||||||||||
catcatttgtctcagaaaaatttagaaaaaagagggcctttttcctctcaatgcctggggactt--tatttttttctgtaatgttc--atattcgaac-ttgcagGCTTATTCTACTGTTGGGACACCAGACTATATCGCTCCAGAAGTTTTATTGAAGAAAGGTTATGGGATGGAATGTGATTG
upper sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S86_100V6.1 (Physcomitrella patens), 3'ss of exon 5
---------------------------------------------------------------------------------------------------ttcat---tatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
|||| ||| ||| | | || |||| || ||| || || | ||| || || | | ||| | || | || | | | ||||| ||||| ||||| || || ||||| || || ||||| ||||| || |||||||| |||||||||||||| ||||| ||
gtatgtttacctcttctttttctgcgcattcttctttcctccaaactactccttgatcgtatggttaataaatggtattccagtacctgcgcgcgagaattcacgcgcgtac-attctttttagatatatgacctgtggttt--ttatttttcgaccactagtcaaacat-caagtattaattccaggttttgctcat-cagGCCTATTCAACAGTCGGCACTCCAGACTACATCGCTCCTGAAGTCCTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
upper sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S87_129V6.1 (Physcomitrella patens), 3'ss of exon 5
-------------------------------------------------------------ttcatt-atactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttga-atgtataaatgt-tgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
|||| || || || | | | | | || | | | | || | | | | ||| | || | |||| | | | | ||||| ||||| ||||| || || ||||||||||||||||| ||||| || |||||||||| ||||||||||| ||||| ||
gtaatcttctttgcattccattttgcagtagctcttcgtcctcttcacaatttctgcctttgtcatagatgtcatcttctaggtttgcatacagaggagtgcaagtggcactcca---ttgatcatctgtaatctcaagtattgacacaaagtttcgcattcagGCATATTCAACAGTCGGCACTCCAGATTATATTGCTCCTGAAGTACTGCTGAAGAAAGGCTATGGGATGGAGTGTGACTG
upper sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
lower sequence: PP1S22_429V6.2 (Physcomitrella patens), 3'ss of exon 6
----------------------------------------------------------------------------ttcattatac-tattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgt---gtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
|| || ||| | |||| || | | | | || |||||||| || |||| | | |||| | |||||| | | ||||| ||||| ||||| || || ||||| ||||| ||||| ||||| || |||||||| |||||||||||||| ||||| ||
gtatttctttttgcttacatccttcctccccaacactgttcctgaattatatgttttagtttcagcgtccgggatggcacttgtatacattctctgtagatgtaggacctgcagctcc-atgatgttctactactctttgagcatctagttttcaggttttga-cacaaggtttcaacagGCGTATTCGACAGTCGGCACTCCAGACTATATCGCTCCGGAAGTACTGTTGAAGAAGGGTTATGGGATGGAGTGTGACTG
upper sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ28086 (Selaginella moellendorffii), 3'ss of exon 5
ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
||| || ||| || |||||| ||| || | | | ||| | | ||||||||||| || || || || ||||||||||||||||| |||||||| ||||||| || || |||||||| ||||||||
--------------------------------------gtgcgtagc-ttgtacttccttttgtcccgattttta---tctaagtgttc---tttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTG
upper sequence: GLYMA13G18670.2 (Glycine max), 3'ss of exon 5
lower sequence: EFJ29515 (Selaginella moellendorffii), 3'ss of exon 5
ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
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--------------------------------------gtgcgtagc-ttgtacttccttttgtcccgattttta---tctaagtttcc---tttaacagGCTTATTCAACTGTCGGGACGCCAGATTATATTGCTCCCGAAGTTCTACTGAAGAAGGGATACGGGATGGAGTGTGATTGMapped 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|192315781|gb|FK008491.1|FK008491EST: GCTCACAACAGGAACAACTGCAACATTGGCAAATGAACAGGAGGACACTT GCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTG
genomic: GCTCACAACAGGAACAACTGCAACATTGGCAAATGAACAGGAGGACACTTgtaagttcac ... aatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
tttgtaatttttgaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcattatactattttgtgtatatatgtggatagtgtttaagatagtgttctacatctttttgtgtgtgtttgtaatttttgaatgtataaatgttgcagGCTTATTCCACAGTTGGTACACCAGATTATATTGCTCCAGAAGTTCTTTTGAAGAAAGGTTATGGGATGGAATGTGATTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - ttttgtg
- - - - - - - - - - - - - - -gatagtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gtgtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaatgta