Sequence
atgc intronic sequence ATGC exonic sequencegtacatgtccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
Basic information
species | Glycine max |
transcript | GLYMA03G39290.1 |
intron # | 21 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
lower sequence: LOC_Os01g15020.2 (Oryza sativa), 3'ss of exon 20
gtacatgtccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
||| ||| || | || || | |||| | | | | | || ||| | || || | ||||| ||||||||||||||||||||||| || || || |||||| |||| || ||||||||||| ||||| |||||||| ||||| ||||| |||||||| |
gtaaatgctca-atatcttttttggataa---atacttcaaaattcaggaaattttaattatgcttccttcatg-cagGTGATGACAACATTCATGCCACCACCTCCAGCATCAACCTTTTTAGCATTTCACCCTCAAGACAATAATATCATAGCAATTGGAATGGAAGATTCAACCA
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G416836_T01 (Zea mays), 3'ss of exon 18
gtacatgtccagagatacaaccatgacattcc-atacagccgcaatgtttactgtatacttag--gtttattttctat-cagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
| | ||| | |||| || | | ||| | | | ||| | || | || ||||| |||||||||||||||| |||||||| || || || ||| |||| || |||||||||||||||||||||||||| || || ||||| |||||||| |
---------gtaatgtctaactgttttattctgatgaaattttcagatttcaagaagatttaatcatgcatccttcatgcagGTGCTGACAACATTCATGCCGCCACCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGATAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
lower sequence: GRMZM2G316967_T01 (Zea mays), 3'ss of exon 20
------------------------gtacatg-tccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
|| || |||| | | || || | ||| | | || | | | |||| ||||| |||||||||||||||||||| ||||| || || || ||| |||| || ||||||||||| |||||||||||||| || || ||||| |||||||| |
atctataagcaggtcattagatgcttatataatccataagctggattatataatcttgagaggaaacaaacatggccttaatcatgcatcc---ttcttgcagGTGATGACAACATTCATGCCACCTCCACCAGCATCAACATTTTTAGCATTTCACCCTCAAGACAATAACATCATAGCAATAGGAATGGAAGATTCAACCA
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
lower sequence: AT5G27030.1 (Arabidopsis thaliana), 3'ss of exon 20
--------------------------------------gtacatgtccagagatacaaccatgacattccatacagccgcaatgtttactgtatactt------aggtttattttctat-cagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
| | | | || || | || | | | || || | || | | |||| | | |||| ||||||||||||||||| || ||||| || || || ||| | || ||||| ||||| || |||||| |||| |||||||| ||||| || || || |
gtatatattatctatatgaacttaaaaaaagccacaagatttctaactgaaaatgttctcacactaatctagtaaactcttttggttgttctaatttccacaaaaaaactattggccttatagGTGATGACAACATTCATGCCGCCTCCACCAGCATCAACGTTTTTGGCGTTCCATCCTCAGGACAATAACGTCATCGCCATTGGAATGGAAGACTCTACGA
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
lower sequence: Vv14s0060g01680.t01 (Vitis vinifera), 3'ss of exon 20
gtacatgtccagagat-acaaccatgacattccatacagcc--gcaatgtttactgtatacttaggtttattttctatc---agGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
||||| | | || ||| || | ||| | ||| | | || || | | | || || |||||||||||||||||||| |||| || || || || ||||| ||||| ||||| |||||||| ||||||||||||||||| || ||||||||||| || |
--gtatgtctaaacatcacagttttgcatcttcatcaaatttggcatttgaaatggtttagcatgatgttgctttcatttgtagGTAATGACAACATTCATGTCACCTCCCCCTGCTTCAACCTTCCTAGCCTTCCATCCTCAAGACAATAACATCATAGCCATAGGAATGGAGGATTCTACCA
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
lower sequence: PP1S316_34V6.1 (Physcomitrella patens), 3'ss of exon 20
------------------------gtacatgtccagagatacaaccatgacattccataca-gccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
|| | | | ||| || | | | | ||| | | || || ||| || || | | |||||| ||||| ||||||||||| ||||| || || |||| ||||| || ||||| || ||||| || |||||||| ||||| || ||||||||||||||||
tattaaaaaaattgaagccattttttattattaaaaaattactctgctggtgatgcttgaacatggcagttctgacagttgccttcggattgtgat---tcagGTCATGACGACATTCATGCCGCCACCTCCAGCAGCTACTTTTCTTGCGTTCCATCCCCAAGACAACAACATCATTGCCATAGGAATGGAGGATTCAACAA
upper sequence: GLYMA03G39290.1 (Glycine max), 3'ss of exon 21
lower sequence: EFJ32018 (Selaginella moellendorffii), 3'ss of exon 20
gtacatgtccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
| ||| | || | || | | ||||| |||||| ||||||||||||| ||||| || | || || || ||||| ||||||||||| || || |||||||| ||||| ||||| ||||| ||||
----------------------------gtatgcacatttttccttcttgaccggtgtaagaacttgccatgt-ccagGTGATGACAGCATTCATGCCACCGCCACCAGCAGCAACGTTCCTGGCTTTTCACCCTCAAGACAACAATATCATAGCGATTGGAATGGAAGATTCTACAAMapped 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|22522387|gb|BU081198.1|BU081198EST: TGTCTGCATGTGGTGGAAAGGTTTCGTTATTTAACATGATGACATTCAAG GTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTC
genomic: TGTCTGCATGTGGTGGAAAGGTTTCGTTATTTAACATGATGACATTCAAGgtacatgtcc ... tttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTC
EST:
gi|4293938|gb|AI442119.1|AI442119EST: TGTCTGCATGTGGTGGAAAGGTTTCGTTATTTAACATGATGACATTCAAG GTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTC
genomic: TGTCTGCATGTGGTGGAAAGGTTTCGTTATTTAACATGATGACATTCAAGgtacatgtcc ... tttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
tttattttct CT-rich tract
tttattttctatca 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatgtccagagatacaaccatgacattccatacagccgcaatgtttactgtatacttaggtttattttctatcagGTAATGACAACATTCATGCCACCACCACCCGCCTCTACCTTTCTAGCTTTCCACCCTCAAGATAATAACATCATAGCCATTGGGATGGAGGATTCAACAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT