Sequence
atgc intronic sequence ATGC exonic sequence...gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
Basic information
species | Glycine max |
transcript | GLYMA14G06340.2 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G822591_T01 (Zea mays), 3'ss of exon 1
-----------gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatt--tctaatgcttattgcgtcattttttttattaatttcat--agGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
|| | |||| || | || | | || || || | | ||| | |||| | || || || | ||| || ||| | |||| ||||||||||||||||||||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||||||||| | || | ||||| ||||
gtatacaagtaggagcacatacttgataattttttgtagtatctgctttatagcagagcttctatcactgtgatctatttttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G325285_T01 (Zea mays), 3'ss of exon 14
-----------gggtgttgtgcttg-ttatatgaacttaatgttgatttgctactagtgatcttattga-atttctaatgcttattgcgtcattttttttat-taatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
|| | ||| | || | || | | || || || | | ||| || || || | | | | |||| | | || ||||| ||||||||||||||||||||||| || |||||||| ||||| ||||||||||| ||||| ||||||||||||||||| | || ||||||| ||||
gtatacaagtaggagcacatacttaataatttttttgtagtatctgctttatagcagagcttctatcactatgatctatttttttctcatatctgcttttgtatttttgtttagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAAAATAGAGGATGCTTCAATGAACTCATTGCTCTCATGGAGAGTGGTCTTGGACTAGAACGTGCAC
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G804382_T01 (Zea mays), 3'ss of exon 1
-----------gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
|| | |||| || | || | | ||| || || | | ||| || | | || | ||| |||| |||| | | ||||| ||||||||||||||||||||||| || ||||| || ||||| ||||||| ||| || || ||||||||||||||||| | || | ||||| ||||
gtatacaagtaggagcacatacttgataattttttctagtct--gttttataacagagcttctat-gatctatttctgtctgacatgtctgattttgtatttttgtt-tagGTTGATGACTTGGAAGAAGTCAGTGAGTACTACCAGAATAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G057576_T02 (Zea mays), 3'ss of exon 22
gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattg---aatttcta----atgcttattgc-gtcattttttttattaatttcat--agGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
|| | | | |||| ||| | || ||| | | | |||||| | |||||| || || || | | ||| | | || ||| | |||| || ||| |||||||||||||||| || ||||| |||||||| ||||||| ||| || || ||||||||||||||||| | || | ||||| ||||
--gtatacaagtaggagggcatacttgatgatttttccctagtctttgttttattgcaaagtttctatgatatatttctttctgacatacctgctcttttttttgtttagGTTGACGACCTGGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G395549_T01 (Zea mays), 3'ss of exon 9
----------------------------------------------------------------------gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttcta----atgcttattgc-gtcattttttttattaattt-catagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
| | | | | |||| || || | | | || | || | |||||| || || || | | ||| | | || ||| ||||| |||||| | |||||||||||||| || ||||| |||||||| ||||||| ||| || || ||||||||||||||||| | || | ||||| ||||
gtctgctttgcttgtgttgacgtggaggagttccgtcttgcacaaatatgtggtctcaatattattgttcagatatacaagtaggagggcatacttgatttttccctattctttgttttattgcaaagtttctatgatatatttctttctgacatagctgctctttttttgtttagGTTGATGACCTCGAAGAAGTCAGTGAGTACTACCAGAACAGAGGATGCTTCAGTGAACTTATTGCTCTCATGGAGAGTGGTCTTGGACTTGAACGTGCAC
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: AT3G08530.1 (Arabidopsis thaliana), 3'ss of exon 24
-------------------gggtgttg----tgcttgttatatgaacttaatgttgatttgctactagtgat--cttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
| | | | ||| | | | || | ||| || | || | | || || || | || || || | | |||| | || ||||||||||||| ||||||||||||| || || ||||| |||||||| ||||||||||| | || || || ||||||||||| | ||| | ||||| || |
gtgaatacctgatcttactgagcacaaaagtttccccttacaggttttagatttcaattgtgtatgctttatagcccaatgtatctcatttatttcctg-gttaatcttttggt--gcttaatagGTGGATGACCTGGAAGAAGTCAGCGAGTACTACCAGAACAGAGGGTGCTTCAATGAATTAATCTCACTTATGGAGAGTGGACTTGGGCTTGAACGTGCTC
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: AT3G11130.1 (Arabidopsis thaliana), 3'ss of exon 24
-------gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
| | | | || | || | || | | | || || ||||| |||| | || || || ||||| | ||| ||||||||||||| |||||||||| || || || ||||| |||||||| ||||||||||| | || || || ||||||||||| | || | ||||| || |
gtggataaataacagatcctagttcccgagaaagttttttagttataattgggtttcaatttcaattttgtatgcct-ttttgtaatatttttg--tgctttaatagGTGGATGACCTGGAAGAAGTAAGCGAGTACTACCAGAACAGAGGATGCTTCAATGAATTGATCTCCCTTATGGAGAGTGGACTTGGTCTGGAACGTGCTC
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: Vv13s0067g01290.t01 (Vitis vinifera), 3'ss of exon 24
------------------------------------------------gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaat-----gcttattgcgtcattttttttatt--aatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
| |||| || | || ||| ||| | | | | || || | | ||| || | | || | | | | || ||| ||||| ||||| ||||| ||||| || |||||||| |||||||| || ||||| |||||||||||||| ||||| ||||||||||||||| | || || || || ||||
gtaatgtattgttttttaagggtagggtgggatgataacatcataaaaatggattgttgtttcaaaatttccttctgtatgagcttccaagcctaatgttttcgcttttttattatcaggtctaatttcctagtgtattgatttgaattttgtagGTCGATGATTTGGAGGAGGTCAGTGATTATTACCAGAATAGAGGATGCTTCAATGAGCTAATATCACTCATGGAGAGTGGTCTGGGCTTGGAGCGTGCAC
upper sequence: GLYMA14G06340.1 (Glycine max), 3'ss of exon 24
lower sequence: PP1S147_10V6.1 (Physcomitrella patens), 3'ss of exon 12
-gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaatgcttattgcgtcattttttttattaatttc-atagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
| || ||| | | || | | || ||| | | || ||| | | || |||| ||| | | | ||||| ||||||| || |||||||| ||||||||||||||||| || |||||| |||| |||||||||| || || ||||| ||||| | || || || || || |
ggagtattggattctctggtccaagtagagtatgcattgatttt-gttttctggaaggctagaaaacaattat-ataacatgatcatgctgaatttttgcagGTGGACGATTTGGAAGAGGTCAGTGAATATTACCAGAATAGAGGTCGCTTTGATGAGCTCATCTCACTTATGGAAAGTGGGCTTGGTTTGGAGCGCGCTCMapped 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|6912831|gb|AW394315.1|AW394315EST: CAGAGGAGTNTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAG GTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTC
genomic: CAGAGGAGTTTCGTTTGGCCCAAATTTGTGGACTAAACATTATTATTCAGgtaatatgtt ... aatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgatcttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
tattaat putative branch site (score: 2)
ttattgcgtcattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gggtgttgtgcttgttatatgaacttaatgttgatttgctactagtgatcttattgaatttctaatgcttattgcgtcattttttttattaatttcatagGTGGATGACTTGGAAGAAGTCAGTGAATATTACCAAAACAGAGGTTGCTTCAATGAGCTCATATCTCTCATGGAGAGTGGTTTAGGGTTAGAACGGGCAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGA