Sequence
atgc intronic sequence ATGC exonic sequence...tatatgtggccatctgatttgttatcttcccctccccccaccccctctttttctttttttctaattatcgcttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: Vv18s0072g00300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os12g07020.1 (Oryza sativa), 3'ss of exon 4
--------------------------------------------------tatatgtggccatctgatttgttatcttcccctccccccaccccctctttttctttttttctaattatcgcttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC
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gtgagtttttttatattgattcagctggttatcccttcttggataacctttatatattttttatcaaatt--taaattaattgccttttagctcatttgttccttgattaataactaatg-taaattgccaactgtgtctatgactgcagTGCATGACAAACAATTAGTGAATGACATTCCAGTTGAGAAGCTGTTAGTTCATGATGTACCAGTTGACATTATCTGCACTCCAACTCAGGTCATATTCAC
upper sequence: Vv18s0072g00300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G001904_T01 (Zea mays), 3'ss of exon 2
tatatgtggccatctgatttgttatcttcccctccccccaccccctc--------tttttctttttttctaattatcg-cttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC
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---------ccttcttgattgaaatgcagagctcctaccgttacgttcaaaaaggtatttagtttgtgctagccactaacataaatgccaactatttctatgcttacagTGCATGACAAGCAGTTAGTTGATGACATTCCAGTGGAGAAGCTGCTAGTTCATGATGTGCCAGTTGACATTATCTGCACCCCTACTCAGGTCATCTTCAC
upper sequence: Vv18s0072g00300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA02G08860.1 (Glycine max), 3'ss of exon 5
-tatatgtggccatctgatttgttatcttcccctccccccaccccctctttttctttttttctaattatcgcttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC
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taatgtgcagtcatatttattatctgcttattcttgccatgtgtaaaatttgcaatttgtcttcttttggtatataacatattgagaa-ctacccttgcagTGCATGACTGCCAATTGGTGGACGATATTCCTGTTGAAAAGCTGTTAATCCATGACGTACCAGTGGATATCATTTGTACTCCAACACAGGTCATTTTCAC
upper sequence: Vv18s0072g00300.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G27960.1 (Glycine max), 3'ss of exon 4
-tatatgtggccatctgatttgttatcttcccctccccccaccccctctttttctttttttctaattatcgcttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC
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taatgtgcggtcatattcattatctgtttattcttgccatgtgtaaaatttgcaatttctcttcttttggtatataacatactgagaa-ctacccttgcagTGCATGACTGCCAATTGGTGGATGATATTCCAGTTGAAAAGCTGTTAATCCATGATGTACCAGTGGATATCATTTGTACCCCGACACAGGTCATTTTTACMapped 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|30299597|gb|CB976391.1|CB976391EST: GTTGCAGTACATGGGAGCCATAGATGACACTACTCCTATTGTCACCTCAG TACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCC
genomic: GTTGCGGTACATGGGAGCCATAGATGACACTACTCCTATTGTCACCTCAGgtaagtaggt ... gattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCC
EST:
gi|110385632|gb|EC950176.1|EC950176EST: GTTGCAGTACATGGGAGCCATAGATGACACTACTCCTATTGTCACCTCAG TACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCC
genomic: GTTGCGGTACATGGGAGCCATAGATGACACTACTCCTATTGTCACCTCAGgtaagtaggt ... gattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctttttctttttttctaattatcgcttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC
ttctctg CT-rich tract
ttctttttttctaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tatatgtggccatctgatttgttatcttcccctccccccaccccctctttttctttttttctaattatcgcttcattattttgattctctgattttgcagTACATGATGAGCAATTGGTCGATGATATTCCTGTTGAGAAGCTGTTAATCCATGACGTGCCAGTTGATATTATATGCACCCCAACCCAAGTCATTTTTAC
- - - - gccatct
- - - - - - - - - - - - - - -ccctccc