Sequence
atgc intronic sequence ATGC exonic sequencegtaagtatcctggagaaaataatttgacatttttgtttattttgatctctgtactctcggatttcattctgatcaataggatagtttgtgttgtttcctacttgagttgatgtaaattcataaatcataacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
Basic information
species | Glycine max |
transcript | GLYMA18G27710.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
lower sequence: GRMZM2G135283_T02 (Zea mays), 3'ss of exon 8
gtaagtatcctggagaaaataatttgacatttttgtttattttgatctctgtactctcggatttcattctgatcaatagga-tagtttgtgttg--tttcctacttgagttgatgtaaattcataaatcataacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
||| ||| | ||| || | | ||| |||||| | || |||| || | || || | | ||| | | | | | || | ||||||| | ||||||||||||||| ||||| || ||||| |||||||| || ||||| ||||| || |||||||| || |||||||| | |
--------------------------------------------------gtatggcatgatgaaaac--gataaaaaaaactagcaggtgttgaacctgcttcttgcattaa----aaaccaaaggtt----tagtgatatacttaatattctatagGTTATGTATGATTTTGAGGACAAAATCAATGCTGCTGTCTTTCCTGGTCTGCAAGGTGGGCCTCATAACCATACCATTACTGGCTTGGCTGTTGCGCTCA
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0211g00120.t01 (Vitis vinifera), 3'ss of exon 9
gtaagt-atcctggagaaaataatttgacatttt-----tgtttattttgatctctgtactctcggatttcatt-ctgatcaataggatagtttgtgttgtttccta-cttgagttgatgtaaattcataaatca-taacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
|| ||| | | ||||||| | ||||| | | | |||| || || || | | |||| ||| | | | | || | ||||| | | |||||| | || | | | | ||||| || | ||| | | | ||||| | |||||||||||||| ||||||||||| || ||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||||||||||||||
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcct---actccattactgttttaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatata-tgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0211g00080.t01 (Vitis vinifera), 3'ss of exon 2
gtaagt-atcctggagaaaataatttgacatttttgtttattttgatct--ctgtactctcggatttcattctgatcaataggata---gtttgtgttgtttcctacttgagttgatgtaaattcataaatcat------aacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
|| ||| | | ||||||| | ||||| || | | | | || | | |||| || || | | || || | ||| |||| | |||| || | | | | | |||| || | ||| | | | ||||| | |||||||||||||| ||||||||||| || ||||| || |||||||| ||||| ||||||||||| ||||| ||| |||| ||||||||||||||||
gtgagttgttttaaggaaaatatcattttattttaaccatttctcccttgacctagatatcatactccattactatttattaggcaagtgtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatata-tgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAGGTGGCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0211g00090.t01 (Vitis vinifera), 3'ss of exon 1
gtaagtatcctggagaaaataatttgacatttttgtttattttgatctctgtactctcggatttcattctgatcaataggatagtttgtgttgtttccta-cttgagttgatgtaaattcataaatca-taacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
|| | | | | | | | | | || | ||||| | | |||||| | || | | | | ||||| || | ||| | | | ||||| | |||||||||||||| ||||||||||| || ||||| || |||||||| ||| | | ||||||||| ||||| ||| |||| ||||||||||||||||
------------------------------------------------------tcactactatttattaggcaagt--gtctgcttcttttgttactgaacttgaggttatattgttggacgtggaactaacatttatactttatata-tgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
lower sequence: Vv00s0211g00070.t01 (Vitis vinifera), 3'ss of exon 9
gtaagtatcctggagaaaataatttgacatttttgtttattttgatctctgtactctcggatttcattctgatcaataggatagtttgtgttgtttcctacttgagttgatgtaaattcataaatca-taacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
|| | | | | | ||| | | || | | | | ||||||| | || | | || | ||||| || | ||| | | | ||||| | |||||||||||||| ||||||||||| || ||||| || |||||||| ||| | | ||||||||| ||||| ||| |||| ||||||||||||||||
------------------------------------------------------tcact-actatttattaggcaagtgtctgcttcttttgctattgaacttgaggttatattgttggatgtggaactaacatttatactttatata-tgtgaagGTTTTGTATGACTATGAAGACAAAATCAATCAGGCTGTCTTTCCTGGACTTCAAAGTGCCCCTCACAATCACACAATTGCTGGCTTAGCTGTTGCATTGA
upper sequence: GLYMA18G27710.1 (Glycine max), 3'ss of exon 10
lower sequence: PP1S79_54V6.1 (Physcomitrella patens), 3'ss of exon 9
gtaagtatcctggagaaaataatttgacatttttgtttattttgatctctgtactctcggatttcattctgatcaataggatagtttgtgttgtttcctacttga--gttgatgtaaattcataaatcataacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
| || | | || | || |||| | | || | | | || | |||| | || ||| || | | | || ||| | || || | || || |||||||| |||||||| || |||||||| || ||||| |||||||| |||||||||||||| ||| | || | |||||||| ||||
---------------------------------------------------tgtcttc--actccaacgaaagca-taggggcgatgctggtctcgcgtatgcggaggttggt-tacatttcagctgaatgtttctgatccatcctgc--tgtgcagATTTTCTACGACTATGAAGACAAAATTAATGCTGCTGTTTTTCCAGGACTACAAGGGGGTCCTCACAACCACACCATTGCAGGACTTGCTGTTGCCTTGAMapped 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|120533930|gb|EH262063.1|EH262063EST: TGATATTCTACAGAAAAGGCGTTAAAGAAATTAACAAACAAGGAAAAGAG CTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
genomic: TGATATTCTACAGAAAAGGCGTTAAAGAAATTAACAAACAAGGAAAAGAGgtaagtatcc ... caatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cttgagttgatgtaaattcataaatcataacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
tcataac putative branch site (score: 2)
ttcttcttgc putative PPT
atgtaaattcataaat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtatcctggagaaaataatttgacatttttgtttattttgatctctgtactctcggatttcattctgatcaataggatagtttgtgttgtttcctacttgagttgatgtaaattcataaatcataacagttgttcttcttgcaatttgaagCTATTGTATGACTATGAGGACAAAATCAACCAAGCTGTTTTCCCTGGACTGCAAGGGGGCCCTCACAACCACACTATTACTGGTTTAGCTGTTGCATTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT