Sequence
atgc intronic sequence ATGC exonic sequencegtatgaatctatgacttcaattcatcatactgccttataatttctatacaaattgttgtttaatttattgtttgtaaatacatctatacagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGGATGTCTAAGGTCTAGCAAAGGTCCATGGAATGATCCTGATATCATGAAA
Basic information
species | Glycine max |
transcript | GLYMA16G17830.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 7
lower sequence: GRMZM2G010834_T01 (Zea mays), 3'ss of exon 6
gtatgaat-ctatgacttcaattcatcatactgccttataatttctatacaaattgttgtttaattta--ttgtttgtaaatacatctat-----acagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGGATGTCTAAGGTCTAGCAAAGGTCCATGGAATGATCCTGATATCATGAAA
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gtattttttctattacaaccatattaagcataatttctcgatcataatgattatgtcccattagcttagattgtgtgtgttttcttttgatgttggtagTCAACTTCCTGAATTTTTGGGGGGGACATGCACTTGTGCTGCTGTGGGAGGATGTATGAGGTCTAACAAAGGTCCATGGAATGATCCAGATATTATGAAG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 7
lower sequence: Vv19s0015g01160.t01 (Vitis vinifera), 3'ss of exon 8
----gtatgaatctatgacttcaattcatca-tactgccttataatttcta-tacaaattgttgtttaatttattgtttgtaaatacatct----atacagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGGATGTCTAAGGTCTAGCAAAGGTCCATGGAATGATCCTGATATCATGAAA
|| | | | | | || | | |||| | || | ||||||| | | | ||||| || || || || | | | || | |||||| |||| ||||| |||||||| | || |||||| || || ||||| || || ||||||| ||||||||||||||||||||||| || |||||
gtttgtgtttcacgctcattctgttttgttaatactccattttgatttctaattctatttgttccttgcatttttcttcattttttccccttcttgttcagTCAACTGCCTGACTTCTTGGGTGGCTCTTGCACATGTGCTACTGATGGTGGGTGCCTGAGGTCTAATAAAGGTCCATGGAATGATCCTGAAATAATGAAG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ21359 (Selaginella moellendorffii), 3'ss of exon 6
gtatgaatctatgacttcaattcatcatactgccttataatttctatacaaattgttgttta-atttattgtttgtaaatacatctatacagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGGATGTCTAAGGTCTAGCAAAGGTCCATGGAATGATCCTGATATCATGAAA
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------------------------------------gtaatatctg-aaacatgattgtatgcataaatttgacgtgttttc-ttcatacagTCAGCTGCCAGAGTTTATAGGTGGTACGTGCACATGTCCTGGAGAAGGAGGATGTATGAGATCTGATAAAGGACCTTGGAAGGATCCAGAGTTATTGAAG
upper sequence: GLYMA16G17830.1 (Glycine max), 3'ss of exon 7
lower sequence: EFJ23906 (Selaginella moellendorffii), 3'ss of exon 6
gtatgaatctatgacttcaattcatcatactgccttataatttctatacaaattgttgttta-atttattgtttgtaaatacatctatacagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGGATGTCTAAGGTCTAGCAAAGGTCCATGGAATGATCCTGATATCATGAAA
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------------------------------------gtaatatgtg-aaacatgattgtatgcataaatttgacgtgttttc-ttcatacagTCAGCTGCCAGAGTTTATAGGTGGTACGTGCACATGTCCTGGAGAAGGAGGATGTATGAGATCTGATAAAGGACCTTGGAAGGATCCAGAGTTATTGAAGMapped 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|9566139|gb|BE475648.1|BE475648EST: GTTCTTGAACCTAAATCTTTATGTAAATTACTGGATATCATTGACTCTAG TCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGG
genomic: GTTCTTGAACCTAAATCTTTATGTAAATTACTGGATATCATTGACTCTAGgtatgaatct ... atctatacagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ataatttctatacaaattgttgtttaatttattgtttgtaaatacatctatacagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGGATGTCTAAGGTCTAGCAAAGGTCCATGGAATGATCCTGATATCATGAAA
gtttaat putative branch site (score: 4)
tatacaaattgttgtt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgaatctatgacttcaattcatcatactgccttataatttctatacaaattgttgtttaatttattgtttgtaaatacatctatacagTCAGTTGCCAGACTTTTTGGGTGGAACATGTACATGTCCTGGAGAAGGTGGATGTCTAAGGTCTAGCAAAGGTCCATGGAATGATCCTGATATCATGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA