Sequence
atgc intronic sequence ATGC exonic sequence...gatcttttcgtaggttatgattataaatcaagctaatatattccttttttttgcttaccatatattagtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
Basic information
species | Glycine max |
transcript | GLYMA02G47270.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os11g16370.1 (Oryza sativa), 3'ss of exon 7
-------------------------------------------------------gatcttttcgtaggttatgattataaatcaagctaatatattccttttttttgcttaccatatattagtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
| | || | ||| | | | || | | | || || || | | | |||| ||| || ||| || | |||||||| || ||||| ||||| |||||||| ||||| || || || |||||||||||||||||||| || || || || || |||||||| |||| || |
gtaacatggtcacatctattactgtttttgtttttcactagttctgtttttatttaacatgtttacaaaatattagttgttacttgttaggtacagacttccttgatgattcatttttgaaattaaccattta--atgctattccttttttacagTATTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGATAATGATGTTGCGA
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
lower sequence: LOC_Os02g17320.1 (Oryza sativa), 3'ss of exon 7
---------------------------------gatcttttcgtaggttatgattataaatca-agctaatatattccttttttttgcttaccatatattagtaactgtttctta-taatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
| | |||| | ||| ||| ||||| || | || | | | ||| | | | | || | |||| | || || | | ||||| || || ||||| ||||| |||||||| ||||| || || || |||||||||||||||||||| || || || || || | |||||| |||| || |
gttacatggtcacatacctttttactcactagagctgtttttatttaacatgtttacaaatcttagttgttaggtcagatctccttgatgattcttttttgaaattaaccacttaattctacttatgttttacagTACTCAAAGTTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACCAAGAAGTATGCTGATATTATCATCCCACGAGGTGGCGATAATGATGTTGCAA
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G034143_T01 (Zea mays), 3'ss of exon 7
-----------------------------------------------gatcttttcgtaggttatgattataaatca-----agctaatata---ttcctttttt-ttgcttaccatatattag--taactgtt----------tcttataatat-------------atacttgat-gcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
| | ||| | ||| ||||| || | || | |||||||| ||| | | || |||| || || |||| || ||||| |||||| || | | |||| ||||| || |||||||| ||||| |||||||| ||||| || || || || ||||||||||||||||| || || || || || |||| ||| ||||||| |
gttacaaagcttcctctattgcaatttttgttgtgcatcaaatctaacaacatttagcgggtcttgattctatagcattttcatctaatataatattcttgtcttgttgcatagtgtacattaagctatctgttgtctactcattcttatcattttttggctaataaaacacttttccacagTACTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATATTATCATCCCACGAGGTGGAGACAATGATGTGGCAA
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G169462_T01 (Zea mays), 3'ss of exon 6
----------------------------------------------------------------------------gatcttttcgtaggttatgattataaatca-agctaatatattccttttttttgcttaccatatattagtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
|||| | | || | | | || | | || | || | | || ||| | | || | | | || | || | || |||| || |||||||| ||||| |||||||| ||||| || || || || ||||||||||||||| | || || || || ||| |||| ||| ||||||| |
gttacgaagcttcctctattgcaattttgttgtgcatcaaatctaataacgtttagcagaccttgtgtagcatttttatctaataaaatattcttgtcttgttgcataatttatgttaagctatctgttatctactcttttttgctgtttttggctaacaaatctttttttccacagTTCTCAAAATTTGTTAAGCCTGCTTTTGAAGACTTCATCCTCCCAACGAAGAAGTATGCTGATGTTATCATCCCACGCGGAGGAGACAATGATGTGGCAA
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
lower sequence: AT4G26510.2 (Arabidopsis thaliana), 3'ss of exon 7
---------------------------------------------------------------------------gatcttttcgtaggttatgattataaatcaagctaatatattccttttttttgctta---ccatatattagtaactgtttcttataatatata-----cttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
| || | | | | | || | | ||||| || | | | | |||| || || | | | ||||| || | ||||||||||| || || ||||||||||| |||||||||||||| |||||||| || ||||| ||||| ||||| || || || ||||| | ||||||||||| ||||
gttagcccgtcttagtattgttactgtatatattatcatcaagaacaacaagaaatggtttacctcttgcattttaaatattacattgctctgatctgtatgtttttttctcatattagttcggcgttttcaaatctatatgtttctacccatattttatatgatgtcaaccttttgatgcagTACTCAAAGTTTGTGAAGCCTGCTTTTGATGACTTCATTCTTCCAACGAAGAAATATGCAGATATTATAATCCCTCGTGGTGGGGATAATCATGTAGCTA
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0015g01730.t01 (Vitis vinifera), 3'ss of exon 7
gatcttttcgtaggttatgattat-aaatcaagctaatatattccttttttttgcttaccatatatta-gtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
| | |||||| || | || | | || | | ||| ||| | | | || | | | ||| | || || ||| ||||||| || |||||||||||||| ||||||||||||||||| ||||| || ||||||||||| ||||||||||| ||||||||| |||| |||||||| || |
-tttaacttagaggttaatgcaatcagattgcttttcagtttttatgcatgttgtatacttcctttaatgttaataatcctt-ttatttaatcttagtgcagTACTCAAAATTTGTGAAGCCAGCTTTTGATGACTTTATACTTCCAACAAAGAAGTATGCAGATATCATTATTCCCCGTGGAGGAGACAATCATGTAGCCA
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S19_94V6.1 (Physcomitrella patens), 3'ss of exon 6
gatcttttcgtaggttatgattataaatcaagctaatatattccttttttttgcttaccatatatt-agtaactgtttcttataatatatacttg-atgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
|| | | | | || || | || | | || | | || | |||| | | | | || | | | || | |||||| | || ||||||||||| || |||||||| |||||| | || || ||||||||||| ||| |||| ||||||||||| |||| |||||||||||||
gaccatcccagccttgttgtccatgg--cgtcttagtgcgaacacttcgatctcgtagcttatacggaatgaagatgaactaacttctggaggtgtacgcagTACGCAAAGTTTGTGAAGCCAGCGTTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGAGGAGACAATCATGTGGCTA
upper sequence: GLYMA02G47270.1 (Glycine max), 3'ss of exon 7
lower sequence: PP1S488_8V6.1 (Physcomitrella patens), 3'ss of exon 6
gatcttttcgtaggttatgattataaatcaagctaatatattccttttttttgc--ttaccatatatt-agtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
| | | | ||| | | | | || || | | | || | ||||| | | || || | | | ||| |||||||| | || ||||||||||| || |||||||| |||||| | || || ||||||||||| ||| |||| |||||||||| |||| ||||||||||| |
--gccatctgaatcctatccgtggcagcgtaatgagtacttttggatcatgtagcgttgtcgcatattgaagagaaacgaattgtattttggatttg-tgcagTATGCAAAGTTTGTGAAGCCAGCATTTGATGATTTTATTTTGCCAACAAAGAAGTATGCGGATGTCATCTTACCCCGTGGTGGAGACAATCATGTGGCAA atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tttttttgcttaccatatattagtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
atatattagtaactgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gatcttttcgtaggttatgattataaatcaagctaatatattccttttttttgcttaccatatattagtaactgtttcttataatatatacttgatgcagTATTCTAAATTTGTGAAGCCGGCTTTTGATGACTTTATTCTTCCCACCAAGAAGTATGCTGATATCATTATACCCCGTGGAAGAGATAATCATGTGGCTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - ggttatg
- - - - - - - - - - - - - - caagcta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtttc