Sequence
atgc intronic sequence ATGC exonic sequence...cagtcagcttattcatgtcaattgcgatggtcagtctctatcagagtgaatcatcaatttccatgtccatgatttctttttgaactactcaattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG
Basic information
species | Glycine max |
transcript | GLYMA15G06380.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G129155_T01 (Zea mays), 3'ss of exon 12
-----cagtcagcttattcatgtcaattgcgatggtcagtctctatcagagtgaatcatcaatttccatgtccatgatttctttttgaactac-tcaattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG
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accggctataagtttatttg-gtcatctgt-ataattgtttgcttgcattgacctttcttgttttccttattcat----tcactagcaacaatgttaattgtgcagGAAGATTACATAAACACGTCACACCCAAATTTTATTGGTGGCAGCAAGGCTGTTGAGCAAGCACAGCAGCAAGTTAGGTCTGCCAAAATGTCAGCAGCGG
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G180335_T03 (Zea mays), 3'ss of exon 4
-----cagtcagcttattcatgtcaattgcgatggtcagtctctatcagagtgaatcatcaatttccatgtccatgatttctttttgaactactcaattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG
| | || ||||| | |||| ||| ||| | | || || | | | ||||| | | ||| | || | || | |||| ||||| || ||||||||||| || ||||||| |||||||||||| |||||||| | || ||| ||||| | ||| | | || | |
aaatcgactaagtttattta-gtcatttgt-atgattgtttgctcgcattgacctttcttgttttccgtattcat--tcactagcaacaatatt-aattgtgcagGAAGATTACATAAACACATCGCACCCAAGTTTTATTGGTGGCAGCAAGGCTGTTGAGGAAGCACAGCAGCAAGTTAGGTCTGCCAAAACGTCTGCAGTGG
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 12
lower sequence: AT4G33650.1 (Arabidopsis thaliana), 3'ss of exon 12
-----------------------------------------------------------------------------------cagtcagcttattca--tgtcaattgcgatggtca-gtctctatcagagtgaatcatc--aatttccatgtccatgatttctttttgaactactcaat----tctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG
|| | ||| || | | | | ||| | || | | || | | | || | | | |||| | | | | | ||| | |||||||||| |||||||||||||| || ||||||||||||||||||| |||||| | ||| || || || ||||| || ||| || | || |
gtctgtataatgaattgaaaatcctacgttgagttgagtttctctattgtgtataaagagcccagactaatatgttggttgattagggaccttttttaatcttgagcagtgatttcctcgtttttgattgattagtttctttgaactaaagtattagtgatggtatcataatttcttgaatgtcgtttgcagATGGATTACATAAACACTTCACATCCAAATTTTATTGGTGGAACCAAGGCCGTGGAAGCTGCAATGCATCAAGTGAAGTCTTCGAGGATTCCCCATCCTG
upper sequence: GLYMA15G06380.1 (Glycine max), 3'ss of exon 12
lower sequence: Vv03s0038g00970.t01 (Vitis vinifera), 3'ss of exon 13
-cagtcagcttattcatgtcaa--ttgcgatggtcagt-ctctatcagagtgaatcatcaatttccatgtccatgatttctttttgaactactcaattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG
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caaaccaaaaaaagaaaaaaaaagtagcaattgtatgcacttcatcaaagttaagt----gttttcttgacaatggtctcagtctaagcaattctattctgtagATGGACTACATAAATACTTCACACCCAAATTTTATTGGTGGAAGTAAAGCTGTGGAGATGGCATTGCAACAGATTAAGTCCTCTAGGCTGCCTGTACCTGMapped 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|193351152|gb|FK316728.1|FK316728EST: AAGGCCTTGAACCCTCAGAGAACATGATTGCGCACCTCATAGAAATGGAG ATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCA
genomic: AAGGCCTTGAACCCTCAGAGAACATGATTGCACACCTCATAGAAATGGAGgtatgcacca ... aattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCA
EST:
gi|208142641|gb|GD943997.1|GD943997EST: AAGGCCTTGAACCCTCAGAGAACATGATTGCACACCTCATAGAAATGGAG ATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCA
genomic: AAGGCCTTGAACCCTCAGAGAACATGATTGCACACCTCATAGAAATGGAGgtatgcacca ... aattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaatcatcaatttccatgtccatgatttctttttgaactactcaattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG
atttcttttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cagtcagcttattcatgtcaattgcgatggtcagtctctatcagagtgaatcatcaatttccatgtccatgatttctttttgaactactcaattctgcagATGGACTACATAAACACTTCCCACCCAAATTTTATTGGTGGAAGCAAGGCATTAGAAATAGCTGCACAGCAGACCAAGTCGTCTAGGGTTGCTATACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - tcatgtc
- - - - - - - - - - - tgcgatg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtcc