Sequence
atgc intronic sequence ATGC exonic sequence...aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
Basic information
species | Glycine max |
transcript | GLYMA13G01160.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g35470.3 (Oryza sativa), 3'ss of exon 2
aaagaagattttatttcttattaatcataatccatctacttgtttctaattta--tatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
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-taaattttttttgtgtatatccttgaaattgcaaaaatatgtttgtatcttagttgctcgatttagaggttgctcacttaacaaatg-acacatattgcagTGTCATTGTGGAAGCTCTTAAGGTGGATAGTTTGCAGAAGCTTTGTTCATCACTGGAGCCAATTCTTCGTAGAGTT
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os02g08120.2 (Oryza sativa), 3'ss of exon 2
aaagaagattttatttcttattaatcataa---tccatctacttgtttctaatttatatttattgttagtttcctataattgatt--gatacacatattt---tgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
|| | || | | ||| || | | | | | || | | ||||| | | || ||| || | | | | | ||| |||||||| ||||| ||||| | |||||||| ||| |||||| |||||||||||| | ||||| ||||||||||||||
--------ccttgcgtgttcattactgtaaagctcaacatgtgagaaggtgaattgcgtcttttgttcttctgtcatgattttttccgcttcgcctctttctctgcagTGTTATTGTTGAAGCATTAAAGGTGGATAGTCTGCAGAGGCTTTGCTCATCACTGGAACCAATTCTTCGTAGAGTG
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G054109_T01 (Zea mays), 3'ss of exon 2
---aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
||| |||| | | | | | | | ||| || | |||| | | | | ||| | || || | | | ||||| |||||| |||||||||||||||||| |||||||||||||||| || || ||||| | || |||||||| || ||||||
attttcttagagtttagtgataagttacagtttttaatccaccacccttcaattcaaactacaaatatatttgttgc--ttagttaacgaa-acatttttcagTGTCATTGTGGAAGCTCTCAAGATGGACAGTTTGCAGAAACTCTGTTCATCGCTCGAGCCCATTCTCCGAAGAGTT
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G113453_T01 (Zea mays), 3'ss of exon 2
--------aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
| ||| |||||| | | | | | |||||| | | || || | ||| ||| ||| | || | | | | ||||| |||||| |||||||||||||||||| |||||||||||||||| || || ||||| | || || ||||| || ||||||
aagtaaatttggtagagtttattggtaggttctggtttttgatctaccgctcttcaaactacaaatat-gtttgttgctta--gctaacgaa-----acatttttcagTGTCATTGTGGAAGCTCTCAAGATGGACAGTTTGCAGAAACTCTGTTCATCGCTTGAGCCTATTCTCCGAAGAGTT
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G018837_T04 (Zea mays), 3'ss of exon 2
-------aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
|||||||| ||| | |||| | | || | || | ||| ||| | ||| | | | || |||||||| ||||| ||||| | |||||||| ||| |||||| ||| |||||||| || ||||| ||||||||||||||
cttgcttgcttggcgttttattttaacttattaataacagaataatcggtgacctatc-acattct------atttgttgtaaacggtctgtctgtctaccatgcagTGTTATTGTTGAAGCGTTAAAGGTGGATAGTCTGCAGAGGCTCTGCTCATCATTGGAACCAATTCTTCGTAGAGTA
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: AC202073.4_FGT001 (Zea mays), 3'ss of exon 1
---aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
|| |||| || || | | | | | | | | | | | | ||| | | |||| ||| | | ||||||||| ||||| ||||| |||||||| ||| |||| || |||||||||||||| | ||||| ||||| || ||| ||
gtaaatcaagaccaccattgtt-tcagttgtgctgttttgtgagaatcgaagatcgtcctagtccttaccatgccttaatatatt--ttcctgatgattgcagTGTCATTGTAGAAGCACTCAAGGTAGACTGTTTACAAAAGCTTTGCTCATCACTGGAACCAATTCTGCGCAGAATT
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G451882_T01 (Zea mays), 3'ss of exon 2
aaagaagattttatttcttattaatcataatccatc-tacttgtttctaatttat-atttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
| | || || || | || | | | || | | | || | || | ||| | | ||| | || | | || |||||||| ||||| |||||| | ||| |||| ||| |||||| ||| |||||||| | ||||| ||||||||||||||
--tggctctcttgcttgtttggcgttttattttaacgtattaataacaaaataatgacctatcacattctagttgtaaataatctctctatctaccctgcagTGTTATTGTTGAAGCTTTAAAGATGGATAGTCTGCAGAGGCTCTGCTCATCACTGGAACCAATTCTTCGTAGAGTA
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT2G18750.1 (Arabidopsis thaliana), 3'ss of exon 2
-------------------------------------------------aaagaagattttatttcttattaatcata-atccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatatt-ttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
||| | | ||| || || | || | | || | || |||||| ||||| || | | | | | | | | || ||||||||||||||||||||| | ||| |||| ||||| |||| |||||| || ||||| ||||| |||||||| ||||
gtaatttgtgttgatgcttgtaatttttctgattattgattatggcgttgttgaatctgtaattgatttgtagttgtatgaatgaaaaaagggttgttatgtatattgattgtctgtggatt-tgagaaagttgtgtatgtgttattgcagTGTAATTGTGGAAGCCTTGAAGATGGATAGTTTACAGAGGCTTTGTTCTTCTTTGGAACCGATTCTTCGCCGAGTG
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G57580.1 (Arabidopsis thaliana), 3'ss of exon 2
aaagaagattttatttcttattaatcataatccatctacttgtttcta-atttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
|| || ||||| ||| | | ||| || | |||||||| | || | | || ||| || ||| || || |||||| ||||| || ||||| || || || |||||||||||||||||||| ||||| ||||| ||||| || |||||
--gtaattcactagttcttcttactgaaaatatatacaactgtttctacaaaaatctctgactttggttatctt---ttggtttgcac----------cagTGTGATTGTTGAGGCTCTGAAAGTAGATAGTTTGCAGAAGCTTTGCTCCTCTTTGGAACCTATTCTCCGCCGAGTT
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: AT4G25800.1 (Arabidopsis thaliana), 3'ss of exon 2
aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
|| ||| | | | |||| || | | | | |||||| | | || | | || | | | |||| || | | ||||||| ||||| || ||||| || || ||||||||||||||||||||||| ||||| ||||| || || || |||||
----gtgagtttctctgattttaaccagattgtttttgaaagtttcttagtattaaagactttt--tctggtcctattgctttttgt-----ctgcgcagTGTGATTGTTGAGGCTCTGAAAGTTGACAGTTTGCAGAAGCTTTGCTCGTCTTTGGAACCTATCCTCCGCCGAGTT
upper sequence: GLYMA13G01160.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv11s0052g01380.t01 (Vitis vinifera), 3'ss of exon 1
-aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
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tttgcccttgcctgtttctattaaacctctatgaacgtctcaatttaacacttatttttat-gtcagttctaatatagtaaagaatatatatatcatgcagTGTAATAGTGGAAGCTCTCAAGGTGGATAGTCTGCAGAAACTTTGCTCATCCTTGGAACCTATTCTTCGTAGAGTTMapped 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|193510156|gb|FK467550.1|FK467550EST: GAGGGTGGAGAAGATGATCAGCCCGAACGAAAGAGGCCTGCTCTTGCCAG TGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATC
genomic: GAGGGTGGAGAAGATGATCAGCCCGAACGAAAGAGGCCTGCTCTTGCCAGgtaaattaat ... tattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATC
EST:
gi|208024507|gb|GD825509.1|GD825509EST: CCCGAACGAAAGAGGCCTGCTCTTGCCAG TGTAATTGTGGAAGCTCTCAA
genomic: CCCGAACGAAAGAGGCCTGCTCTTGCCAGgtaaattaat ... tattttgcagTGTAATTGTGGAAGCTCTCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
ttatatttattgttag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aaagaagattttatttcttattaatcataatccatctacttgtttctaatttatatttattgttagtttcctataattgattgatacacatattttgcagTGTAATTGTGGAAGCTCTCAAGGTGGACAGTTTGCAGAAGCTTTGCTCATCTTTAGAACCCATTCTTCGTAGAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - - - - - - - - - - - - - - -ccatcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -atacaca