Sequence
atgc intronic sequence ATGC exonic sequence...ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
Basic information
species | Glycine max |
transcript | GLYMA19G42960.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g47180.1 (Oryza sativa), 3'ss of exon 6
-----------------------ttctaatgaactcttatt---ttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
||| || | || || || || | | | || || || | | || || || ||| | | | | ||| ||| | |||| |||| | ||||| || ||||||||||| ||||||||||| |||||||| ||||| |||||||| ||||| | |||| | |||||| || | ||||
gtatgtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagct--cact-cgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g47180.2 (Oryza sativa), 3'ss of exon 6
-------------------ttctaatgaactcttatt---ttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
||| || | || || || || | | | || || || | | || || || ||| | | | | ||| ||| | |||| |||| | ||||| || ||||||||||| ||||||||||| |||||||| ||||| |||||||| ||||| | |||| | |||||| || | ||||
gtgcttttttttggctgatttcagttgctcatttgttcatttgcatgatccgccacaatcagaaacatactcctagaacaatgttaagctcacagct--cact-cgatcgtacaacttgcagAAAAGAAGACTAATAACACATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCACATCAGGATGGCGCACTTGGATATCCTTTGGGTTGTTCAA
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g22700.1 (Oryza sativa), 3'ss of exon 5
---ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGG-ACAAGTTGGTTTTCCTTTAGGATCTTCAC
|| ||| | ||| ||| | || | | | | | | | | ||||||| | | |||| | | | ||||| ||| | || | || ||||||||||| || |||||||| |||||||||||||| || ||||| ||||| | | || | || | ||
ggtctcatttgatttactatggcccaaaatggagcccggcactctcttaatgtaaattttgcaatgtc--tctaatttgtcccatttatttat-atcttacagAAAAGGAGATTAGTAACACATGCAAATGCAAAAAGCAAGAGTGAAAAGTTTCCTCCTCCGCATCAGGATGGTGCGGTCTCTTTGGTTTCTACAAATCACA-
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G084347_T01 (Zea mays), 3'ss of exon 6
--ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgta--acagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
||| || | | | | ||| || ||| || | ||| | | |||| | | | | || || | ||| || || ||||| |||| | | || |||||||||||||| |||||||||||||||||||| ||||| |||||||||||||| |||||| | || || | |||||
gagtcttatcagccatggtc---caaaaggaagcccatactaccataaa-gcaaactttgcagtatcgctgatttgtgctaatccttttttttccttaatacagAAAAGAAGGTTTATTACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCCTTGGATGCTTCAA
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G333433_T01 (Zea mays), 3'ss of exon 6
-----------------------------------------ttctaatgaactcttattttacaatagaaagtatatgcat-gaatatgcatccagtcaaaagtaaagattaaatttgttac----tatgatttcttgtgta---------acagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
|| ||||||| | || || || | || | ||| | | || || | | | | | || ||| | | || | |||| || | | ||||| |||| | | || |||||||||||||| |||||||||||||||||||| |||||||| ||||| || || | || ||||| || || | |||
gtatgctaattccttatttatttcagttacttagcagttcattggcatgaacttct---ttgca-tataccgtgt-tgcgtagcatctggacctggacgggtgccaaaatttcgtctcttgcctaacgcgattctttttcttctctcctctacagAAAAGAAGGTTGATAACTCATGCAAATGCTAAGAGCAAGAGCGAAAAGTTCCCTCCACCGCATCAGGACGGCGCGCTCGGCTTTCCCTTGGGCTGTTCGA
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM5G873277_T01 (Zea mays), 3'ss of exon 6
--------------------------------------ttctaatgaactc-ttattttacaatagaaagtatat-gcatgaatatgcatccagtcaaaagtaaagatta----aatttgtta-ctatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
|| |||||||| || || | | | ||| || | | | | || | | || |||| | | || | | |||| | || |||| |||| | |||| |||||||||||||| ||||||||||| |||||||| ||||| || ||||| ||||| | |||| ||||| || || | |||
gtacattcctatatttatttgagttacttagcagttcattggcatgaactcgtttgcatatactgtgttgcgtatcatctggaagggtgccaaatcttgtctcttggctaacacaattcttcatcttttctctcttatcta-cagAAAAGAAGGTTAATAACTCATGCAAATGCGAAGAGCAAGAGTGAAAAGTTCCCTCCGCCGCATCAGGATGGCGCACTTGGATTTCCCTTGGGCTGTTCGA
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G052206_T02 (Zea mays), 3'ss of exon 6
ttctaatgaactcttattttacaatagaaagtatatgc-atgaatatgcatccagt-caaaagtaaaga-ttaaatttgttactatgatttc-ttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC---
||| || | | | ||| || ||| || | || | | || | | || | | || || || | | | ||| | | ||||| | || | | ||||||||||| || |||||||||||||||||||| ||||| |||||||||||||| |||||| | ||||| | |||||
-tcttatcggccatggtc---caaaaggaagcccatactatcataaaacaaactttgcagtatcactgacttgtgcttatccttttttttttgtcttaccacagAAACGAAGGTTCGTCACTCATGCA---GCTAAGAGCAAGAGCGAAAAGTTCCCTCCCCCACATCAAGATGGTGCGGTTGGTGTCCCTTTGGACACTTCAAATC
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G156251_T01 (Zea mays), 3'ss of exon 6
ttctaatgaactcttattttacaatagaaagtatat-gcatgaatatgcatccagtcaaaa--gtaaagattaaatttgttactatgatttcttgt--gtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
| || | | | || | | || || | | | | | ||| | || | || || || ||| | | || |||| | | ||||| |||| | || |||||||||||||| ||||| || || || ||||||||||| || ||||| |||||| ||| ||| | ||||| |
gtgccat-agcccataagtaaactcaggctgtttgtcactttcaaatgttattgcttaatatgatactgaatattgaggtttcca-aatctcttattaacagCAGAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCT---
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G156251_T02 (Zea mays), 3'ss of exon 6
ttctaatgaactcttattttacaatagaaagtatat-gcatgaatatgcatccagtcaaaa--gtaaagattaaatttgttactatgatttcttgt--gtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
|| | | | || | | || || | | | | | ||| | || | || || || ||| | | || |||| | | ||||| |||| | || |||||||||||||| ||||| || || || ||||||||||| || ||||| |||||| ||| ||| | ||||| | |
---ccat-agcccataagtaaactcaggctgtttgtcactttcaaatgttattgcttaatatgatactgaatattgaggtttcca-aatctcttattaacagcagAGGCGACGAATGATAACTCATGCAAATGCAAAGAGTAAAAGTGAGAAGTTTCCTCCTCCGCATCAGGATGGAGGTACGGGTAATCCGCTTGGATCCTATC
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G54610.1 (Arabidopsis thaliana), 3'ss of exon 7
-----ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAG---TTGGTTTTCCTTTAGGATCTTCAC
||||| | ||| | ||| | | | || || | |||| | || | | | | || | | ||| | ||| | |||||||| | ||||||| || |||||||| |||||||||||||| |||||||| |||||||| |||||||| || | ||| | || || || | |
tctgcttctagcata-tctacatacacacacacacacacacacacaaagactgatcctttt---tttacataatcatttctatcttttgact-cttaaaaagcagAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTGCCT---
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT1G54610.2 (Arabidopsis thaliana), 3'ss of exon 7
--------ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGT--TGGTTTTCCTTTAGGATCTTCAC
||||| | ||| | ||| | | | || || | |||| | || | | | | || | | ||| | ||| | |||||||| | ||||||| || |||||||| |||||||||||||| |||||||| |||||||| |||||||| || ||| | | | | || |
tgttctgcttctagcata-tctacatacacacacacacacacacacacaaagactgatcctttt---tttacataatcatttctatcttttgact-cttaaaaagCAGAGAAGGAGATTAATCACACACGCAAATGCAAAGAGCAAGAGCGAGAAGTTTCCGCCACCACACCAAGATGGTGGAGCAATGGGTGTACCATTGGGTG-----
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: AT3G05050.1 (Arabidopsis thaliana), 3'ss of exon 7
ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
| | ||| | || | |||| || ||| | | ||| |||| || || |||| ||| | ||||||| | ||| | ||||| || || ||||| |||||||||||||| |||||||||||||| |||||||| || | | ||||||| | |||||||||
-----gtaagaatttaaaacaaaaaaagaagtgaatctttgattggttaat--gtcttgagtact--ttgaacttgt----------tctcttaaaacagAGGATGCGTATGATCACACACGCGAATGCAAAGAGCAAGAGCGAGAAGTTTCCTCCACCGCATCAAGACGGGTCACTCGGTTTTCAGGTGGGATCTTCAA
upper sequence: GLYMA19G42960.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv14s0030g01260.t01 (Vitis vinifera), 3'ss of exon 9
ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaa--gattaaatttgtta-ctatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
| || || || ||| | | | || | | | || || | | | | || |||||||| | || || || || ||||| ||||||| |||||| | ||||||||||| ||||| ||||| ||||||||||||||||| || || || ||| |||||| || || || || ||||||
---ttgagagcttttgtttcttttttatgtttgcaatcacccgagtccttgcaaccagagttcgattgtttgaatttgttttccgtgtttctttctgaaacagCGAAGACGCCTAATCTCCCATGCAAATGCAAAGAGTAAGAGTGAAAAGTTTCCTCCACCTCACCAGGACGGAGCAGTTGGCTTCCCCTTGGGTGCTTCACMapped 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|207792334|gb|GD764240.1|GD764240EST: AAGCTTTTCCTGCTCCTGAAGCCAATGCTGAGCTTCAATCCAATATTGAT AGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTT
genomic: AAGCTTTTCCTGCTCCTGAAGCCAATGCTGAGCTTCAATCCAATATTGATgtacgttcaa ... tgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTT
EST:
gi|21256192|gb|BQ453080.1|BQ453080EST: AAGCTTTTCCTGCTCCTGAAGCCAATGCTGAGCTTCAATCCAATATTGAT AGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTT
genomic: AAGCTTTTCCTGCTCCTGAAGCCAATGCTGAGCTTCAATCCAATATTGATgtacgttcaa ... tgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
tttcttgt CT-rich tract
aaaagtaaagattaaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttctaatgaactcttattttacaatagaaagtatatgcatgaatatgcatccagtcaaaagtaaagattaaatttgttactatgatttcttgtgtaacagAGAAGACGTCTAATCACTCATGCAAATGCCAAGAGCAAGAGCGAAAAGTTTCCTCCACCACATCAAGATGGACAAGTTGGTTTTCCTTTAGGATCTTCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - aatgaac
- - - - - - - - - - - aatagaaa
- - - - - - - - - - - - - - - - - - gcatgaa
- - - - - - - - - - - - - - - - - - - - - - - gcatcca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaagtaa