Sequence
atgc intronic sequence ATGC exonic sequence...aatattaatcaagctatcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
Basic information
species | Glycine max |
transcript | GLYMA18G08180.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7
------------------------------------------------aatattaatcaagctatcatattctttatcagagtttgatgttaatagctaccattca--atggatttttgtggctgat--tcttatgtaatac--ttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
|||| | || | | || | | || | ||| | | || | || | || ||||||| | | | | ||| || | || || ||||||||||| ||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||||| || || || || || ||||||||| |||| || |
gtaacatggtcacatctattactgtttttgtttttcactagttctgtttttatttaacatgtttacaaaatattagttgttacttgttaggtacagacttccttgatgattcatttttgaaattaaccatttaatgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7
---------------------------------------aatattaatcaagctatcatattct--ttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
|||| | || | | || || | || | || || ||| | | | || || | || | ||||| | || | || ||||| ||||| ||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||||| || || || || || || |||||| |||| || |
gttacatggtcacatacctttttactcactagagctgtttttatttaacatgtttacaaatcttagttgttag-gtcagatctccttgatgattcttttttgaaattaaccacttaattctact----tatgttttacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
---------------------------------------------------------------------------aatattaatcaagctatcatattctt-tatcagagtttgatgttaat--agctaccatt---caatggatttttgtggctgatt--cttatgtaatacttgtt-gcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
|| || ||| | ||| |||||||| | | | | ||| || ||||| | | | | ||| || | | || || || || |||| | ||||| ||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||||| || || || || || ||||| ||| ||||||| |
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaa-tataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
--------------------------------------------------------------------------aatat-taatcaagctatcatattctttatcagagtttgatgttaa--tagctaccattcaatggatttt--tgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
||| |||| || || | | | | || | ||| ||||||| || || || | | |||| ||| || | | | | || |||| ||||||||||| ||||| |||||||| ||||| || || ||||| ||||||||||||||| | || || || || |||||||| ||| ||||||| |
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataattt-atgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
----------------------------------------------------------------------------aatatta-atcaagcta--tcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaata-----cttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
||||||| || || ||| ||| | | | | | | | | || || ||| | | || |||| | ||| ||||||| ||||| ||||||||||| |||||||||||||| ||||||||||| ||||| ||||| ||||| || || || ||||| || ||||||||||| || |
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: AT1G55810.1 (Arabidopsis thaliana), 3'ss of exon 7
aatattaatcaagctatcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgt-tgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
||| | | || || | | || ||| ||| | | | ||| | ||| | ||| | ||||||| ||||| |||||||||||||| ||||| || || || || ||||||||||| || || |||||||| || ||||| || || ||||| ||||| || |
-----------------------gttttgtgtggctgtatattcttgttttgcaaataatttctttatttatgtt-ttcatgtgtgaaactcttatgcagTACTCAAAGTTTGTGAAGCCAGCATTTGAGGATTTCATACTCCCAACAAAGAAATACGCAGATATAATAATTCCCCGAGGTGGTGATAACCATGTTGCTA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
-----aatattaatcaa-gctatcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
|| | || || |||| ||| || |||| ||| ||| | | || ||| | || || | | |||| |||| ||| ||||||| ||||||||||||||||||||||||||||||||||| |||||||||||||||||||| ||||| ||||| |||||||||||||| |||||||| ||||
tttaacttagaggttaatgcaatcagattgcttttcagttttt-atgcatgttg-tatacttcctttaatgttaataatc--cttttatttaat-cttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S370_24V6.1 (Physcomitrella patens), 3'ss of exon 5
aatattaatcaagctatcatattctttatcagagtttgatgttaatagctaccattcaatg----gatttttgtggctgattcttatgtaatacttgtt--gcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
|| |||| | | | || ||| | || || | | | || || | || ||| | || || | | || |||||| || |||||||| || ||||||||||| ||| | | || |||||||||||||| ||| |||| | || ||||||||||| ||||| ||||| |
-----tagccaaggtgtatttttatttgttttttttaaattcttaggtccttcaacttttgttctgcttagtgtacttagtttgcatctcggtgtcattatgcagTACGGGAAGTTTGTGAAACCCGCTTTTGATGATTTTGTGTTACCCACAAAGAAGTATGCGGATGTAATCTTGCCTCGTGGAGGAGACAATCACGTGGCTA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 6
aatattaatcaagcta-tcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgt-------tgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
| || | | | | || | || || || || | || | || | | || | | ||| | | ||| || |||||| |||| |||||||||||||| |||||||| |||||| | ||||||||||||||||| ||| | || |||||||||||||||| ||||||||||| |
------gaccatcccagccttgttgtccatggcgtcttagtgcgaaca-cttcgatctcgtagcttatacggaatgaagatgaactaacttctggaggtgtacgcagTACGCAAAGTTTGTGAAGCCAGCGTTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGAGGAGACAATCATGTGGCTA-
upper sequence: GLYMA18G08180.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S488_8V6.1 (Physcomitrella patens), 3'ss of exon 6
--------aatattaatcaagctatcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
||| || | | | | || | || | | |||| | | | | | || | || | ||| | | |||| ||||||| |||| |||||||||||||| |||||||| |||||| | ||||||||||||||||| ||| | || |||||||||| ||||| ||||||||||| |
gccatctgaatcctatccgtggcagcgtaatgagtacttttggatcatgt--agcgttgtcgcatattgaag----agaaacgaattgtattttggatttgt-gcagTATGCAAAGTTTGTGAAGCCAGCATTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGTGGAGACAATCATGTGGCAA-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|10232146|gb|BE801034.1|BE801034EST: GCAGTTCTTGATCAGT ATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGA
genomic: GCAGTTCTTGATCAGGtagtaaaatt ... ttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tagctaccattcaatggatttttgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
ggctgat putative branch site (score: 4)
attcttatgtaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
aatattaatcaagctatcatattctttatcagagtttgatgttaatagctaccattcaatggatttttgtggctgattcttatgtaatacttgttgcagtATTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATTCTTCCAACAAAGAAGTATGCTGATATAATTATACCCCGTGGAGGAGATAATCATGTGGCCAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - -caagcta
- - - - - - - - - - - - - - - - - - tgatgtt
- - - - - - - - - - - - - - - - - - - - - - - - - -ccattca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gctgatt