Sequence
atgc intronic sequence ATGC exonic sequence...gttgcttttgtattactcgctggttatgctataaattattgttggaaatttatgctgtatttacaattgcctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGAGTTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
Basic information
species | Glycine max |
transcript | GLYMA20G33770.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os10g41370.1 (Oryza sativa), 3'ss of exon 2
--gttgcttttg-----tattactcgctggttatgctat-aaattattgttggaaatttatgctgtatttacaattgcctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGAGTTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
||| | | || || || || ||| | || | | || ||||| | | ||| || ||||| || || || | || | ||| ||| | ||||||| |||||||| || || || |||||||| |||||||| ||||||||||||||||||||| || |||| ||| | ||||| || ||||| ||||
gggttcatctcaacggatactaatctcttgttctactcttatgttgttgttagcagttt---ttggattta-aactgat--aatcctaagaac--atgattgtcacagGTTCTGATATATTCACCGGATGGGAGGTGCCTGTTCAAGTACTTAGCATATGAAAGTGGATTAGGTGTGAAAACTGTTGCGTGGTCACCATGTGGACAGT
upper sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G374969_T01 (Zea mays), 3'ss of exon 2
gttgcttttgtattactcgctggt--tatgctataaattattgttggaaatttatgctgtatttacaattgcctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGAGTTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
| | | || | || | | | | | || || | | |||| | | ||| | || | | ||| ||| || ||||||| |||||||| ||||||||||||||| | |||||||||| ||| ||||||||||| || || || |||| ||| | ||||| || ||||| ||||
-taaactaagaataatacgattatgcaaagatgctaactacaat-gattctttaagaacaaattatttcaagttctgacatctttctttttgtcacttacagGTTCTGATATATTCGCCAGACGGAAGGTGCTTGTTCAAGTATCTAGCTTATGAAAGTGGGTTGGGTGTGAAAACTGTTGCTTGGTCACCATGTGGACAGT
upper sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G07590.1 (Arabidopsis thaliana), 3'ss of exon 2
------gttgcttttgtattactcgctggttatgctataaattattgttggaaatttatgctgtatttacaattgcctaaaacttagtcatttatg--tttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGAGTTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
| | ||| ||||| | | ||| | || || || |||||| ||| | ||| | ||| | | || |||| | ||| |||||||||| ||||||||||| || ||||| || || ||||| || ||||||||| ||||| | || || || | ||| ||||||||||| ||||||||||
gtatgtatcgttttggtattgat-----gctat-ttttagatagttattggaattttgttatgtttggtttgttggagatatctctaaaatttgtaccttttgggcagGTTCTAATTTATTCTCCAGATGGTAGGTGTCTGTTTAAGTACCAGGCATATGAATGTGGACTTGGTGTCAAGACTGTTTCCTGGTCTCCGTGTGGTCAGT
upper sequence: GLYMA20G33770.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv16s0013g01510.t01 (Vitis vinifera), 3'ss of exon 3
gttgcttttg-tattactcgctggttatgctataaattattgttggaaatttatgctgtatttacaattgcctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGAGTTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
| || || |||| ||| || || || | | | || || ||| || || | || || | | || ||||| || ||||||| || || || ||||| || |||||||| | |||||||||||||||||||||||| |||| || || | || || |||||||||||||||||||
-tgatttgtgatattttaagcttcagatactgtacagttgtagtgacaaactattcttggttgaaaaatgaaaagcttaaaatctgcatggtttggtacagGTTCTTATCTACTCCCCAGATGGGAGGTGCCTATCTAAGTATCAAGCATATGAAAGTGGACTAGGTGTGAAGACCGTTTCATGGTCTCCTTGTGGTCAGTMapped 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|207792375|gb|GD765023.1|GD765023EST: CACCTGATGATAGTGCTATAGTGATATGGGATTCACCACTTGATTACAAG GTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGCATCAAGCATAT
genomic: CACCTGATGATAGTGCTATAGTGATATGGGATTCACCACTTGATTACAAGgtaacttcgt ... tttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatttatgctgtatttacaattgcctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGAGTTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
atttatgtttgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gttgcttttgtattactcgctggttatgctataaattattgttggaaatttatgctgtatttacaattgcctaaaacttagtcatttatgtttgatatagGTTCTAATATATTCTCCAGACGGAAGGTGCCTTTTCAAGTATCAAGCATATGAAAGTGGATTAGGAGTTAAAAGTGTGTCCTGGTCTCCTTGTGGTCAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
gttgctt
- - - - - - - - - gctggtt
- - - - - - - - - - - - - tgctata
- - - - - - - - - - - - - - - - - - - ttgttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - tgctgta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -caattgc