Sequence
atgc intronic sequence ATGC exonic sequencegtaagtataaacttttcgctcaatttgcctgaatctagtttttgttgcaataattaacatgacatgggtaatgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
Basic information
species | Glycine max |
transcript | GLYMA20G36110.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os04g41910.1 (Oryza sativa), 3'ss of exon 5
-------------gtaagtataaacttttcgctcaatttgcctga---atctag----tttttgttgcaataattaacat--gacatgggtaatg------tattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
| || || | || | |||| ||| || || || || | ||| || | | | | | || | |||||||||||||||||||||||||||||||||||||||||||||
gtaagttgcttatatctttaaaagcactttgtatgctttgaatgacctatttaacacattcatgattatgtaaatagtgtctggttttgatggtgaatttcttttgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G171660_T02 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------gtaagtataaacttttcgctcaatttgcctga-atctagtttttgttgcaataattaacatgacatgggtaatgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
| | || | |||| |||| | || || | | ||| || | |||||||||||||||||||||||||| || ||||| |||||||||
gtaaattgcttctaccaactaattctatatttcatttctcttatagagatcattttgtttaatgaccatgtaacaaacgcttaattaattggttatttaaaaagtacttgttctgcacttgtgatgctggattccttttgcagATTGTGGAGGTATTTTCCAAGTGCGGAATAATAAAGGAG
upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G353114_T01 (Zea mays), 3'ss of exon 8
-------------------------------------------------------------gtaagtataaacttttcgctcaatttgcctga-atctagtttttgttgcaataattaacatgacatgggtaatgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
| | || | ||| |||| | || || | | ||| || | | |||||||||||||||||||||||||| || ||||| |||||||||
gtaaattgcttctaccaactaactctacatttcatttctcttatagagataattttgtttaatgaccatgtagcaaatgcttaattatttggttatttaaaaagtacttgttctgcacttgtgatgctggatttcttttgcagATTGTGGAGGTATTTTCCAAGTGCGGAATAATAAAGGAG
upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G084716_T01 (Zea mays), 3'ss of exon 5
-------------------------------------------------------------gtaagtataaacttttcgctcaatttgcctga-atctagtttttgttgcaataattaacatgacatgggtaatgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
| | || | ||| |||| | || || | | ||| || | | |||||||||||||||||||||||||| || | ||| |||||||||
gtaaattgcttctaccaactaactctacatttcatttctcttatagagataattttgtttaatgaccatgtagcaaatgcttaattatttggttatttaaaaagtacttgttctgcacttgtgatgctggatttcttttgcagATTGTGGAGGTATTTTCCAAGTGCGAAATAATAAAGGAG
upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G411893_T01 (Zea mays), 3'ss of exon 4
-------------------------------------------------------------gtaagtataaacttttcgctcaatttgcctga-atctagtttttgttgcaataattaacatgacatgggtaatgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
| | || | ||| |||| | || || | | ||| || | | |||||||||||||||||||||||||| | ||||| |||||||||
gtaaattgcttctaccaactaactctacatttcatttctcttatagagataattttgtttaatgaccatgtagcaaatgcttaattatttggttatttaaaaagtacttgttctgcacttgtgatgctggatttcttttgcagATTGTGGAGGTATTTTCCAAGCGCGGAATAATAAAGGAG
upper sequence: GLYMA20G36110.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G074351_T01 (Zea mays), 3'ss of exon 5
-----------------------------------------------------------------gtaagtataaacttttcgctcaatttgcctgaatcta-gtttttgttgcaataattaacatgacatgggtaatgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
| ||| || || | | |||| | || || ||||| | | | || |||| ||| | | ||||||||||| ||| ||||||||| |||||||| |||||||||
gtaaattgcttctaacaactaattatacatttcatttctcttttagagatcgttttgttgaatgaccatgtagcaaattcttaattaattggttatttcataagtacttgttccga-acttctgatgat---ggttttcttttgcagATTGTAGAGACATTTTCCAAGTGTGGAATAATAAAGGAGMapped 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|208154719|gb|GD957536.1|GD957536EST: GTTTATGTCACTGGGTTTGTCCTGAGGATGTTACCACTGATGAA ATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
genomic: GTTTATGTCACTGGG-TTG-CCTGAGGATGTTACCACTGATGAAgtaagtataa ... tgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gcctgaatctagtttttgttgcaataattaacatgacatgggtaatgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
aattaac putative branch site (score: 2)
aataattaacatga 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagtataaacttttcgctcaatttgcctgaatctagtttttgttgcaataattaacatgacatgggtaatgtattgcagATTGTGGAGGTATTTTCCAAATGTGGAATTATAAAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG