Sequence
atgc intronic sequence ATGC exonic sequence...ggactaaaagatagtaaaccctatttttatttagaaaaactagttaaggaaacttcttgctggatttttttttgtctcctaaagatatatcctttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
Basic information
species | Glycine max |
transcript | GLYMA14G03760.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os12g41715.1 (Oryza sativa), 3'ss of exon 4
-ggactaaaagatagtaaaccctatttttatttagaaaaactagttaaggaaac---ttcttgctggatttttttttgtctcctaaagatatatcctttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
|| | | || | | | ||| | ||| | | | || || || || | | ||| | ||| | || | || | |||| ||||||||||| || || |||||||| || || ||||||||| | |||||||||||||| || || ||||||| | ||| | | || ||||
gtgaatgtagtttactgt-cattttttatgtttgaccatatcgaccttaaatactaatttttactataaaatgctttaaat--taattgttcattcatt-tcagGAGCATGCAAAAGGTGGTAAATGCATTGTATTTACACAAACAAAAAGAGATGCTGATCGATTGTCCTACACCATGGGTCGGAGTTTCCAGTGCCAGGCCC
upper sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G565140_T01 (Zea mays), 3'ss of exon 4
ggactaaaagatagtaaaccctatttttatttagaaaaactagttaaggaaacttcttgctggatttttttttgtctcctaaagatatatc--ctttgt-tagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
|| | ||||| | |||| || || ||| | || |||| | | || || | | || || ||||||||||||||||| || |||||||||||||| || ||||||||| | ||||| ||| |||| ||| | | ||| ||||| | ||||||||||
-------gtcggggtttattatatttgtcccattaaaatttaattt------ctttgttcta-atttgctggagcacgttagcaatttgtttgtttcgtgtagGAACATGCAAAAGGTGGCAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAATGTGAGGCGC
upper sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G107984_T01 (Zea mays), 3'ss of exon 4
--------ggactaaaagatagtaaac----cctatttttatttagaaaa--actagttaagg---aaacttcttgctggatttttttttgtctcctaaagatatatcctttgtt--agGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
|| || || || | || ||| | || | | ||| || | || | |||| || | | || || ||| || | |||||||||| ||||| || |||||||||||||| || ||||||||| | ||||| ||| |||| ||| | | ||| ||||| | | |||||||||
gtcaatatagattaggttttattatatttgtcccattaaaacctaattattttccagtgaaagctagtgtttttcttctaatttgttggagcatgttagcaatttatttgttcatgcagGAACATGCCAAAGGTGGTAAGTGCATTGTTTTTACACAAACAAAAAGGGATGCAGATAGATTGTCACACAATATGAGTCGAAGTTTCCAGTGTGAGGCTC
upper sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G22310.1 (Arabidopsis thaliana), 3'ss of exon 4
ggactaaaagatagtaaaccctatttttatttagaaaaacta------gttaaggaaacttcttgctggatttttttttgtctcctaaagatatatcctttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
| | | || | ||||| | | || ||| | | || || | | || | || || | | || ||||||||| ||||||||||| |||||||| || || ||||||||||||||||| ||||| | ||| | |||||| ||| ||||||||| ||||
----gtatgttttctttactttgcttttaagccaattatctgtatcttgttttgattcttcatttttgtttccagtcgtgattttataacatcttctcctttacagGAACATGGCAAAGGAGGAAAATGCATTGTCTTTACCCAAACAAAACGTGATGCAGATCGCCTTGCATTTGGATTGGCAAAAAGCTATAAATGTGAAGCTT
upper sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G22330.1 (Arabidopsis thaliana), 3'ss of exon 4
-------------------ggactaaaagatagtaaaccctatttt----tatttagaaa---aactagttaaggaaacttcttgctggattttttt-ttgtctcc---------taaagatatatcctttgtt---agGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
| |||| || | | ||||| |||| || || | ||||| | || ||| || | |||| | ||| |||| ||| | |||| ||||| ||||||||||| ||||||||||| || ||||||||||| ||||||||||| | |||||| | |||| ||||| | |||||||| ||||
gtatgctttccttactttgctattaaacgagtatgagttaaattttgtgttattcagtaactgagtaagttatttgtgtattttttcggagttgtcagttgtatatggaaagagttaataatatcaattttccttgcagGAGCATGCCAAAGGAGGAAAATGCATTGTTTTTACACAAACAAAACGAGATGCTGATCGCCTTTCATATGCATTGGCTAGAAGCTTCAAATGTGAAGCTT
upper sequence: GLYMA14G03760.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv12s0142g00670.t01 (Vitis vinifera), 3'ss of exon 4
-------------------------------------------------------------------------------ggactaaaagatagtaaacc-ctatttttatttagaaaaactagttaaggaaacttcttgctggatttttttttgtctcctaaagatatatcc---tttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
| | | || | || || || |||| | || || | ||| | || || |||| || | || ||| |||||||||||||||||||||| ||||| || ||||||||||||||||||||||| |||||||||||||| ||||| | |||||||||| | | ||||||||||
gtatgaacccaggacttcattttgtttctttctcctaatttttactgtttccagagctttaggttttctgtatgttaaagtttttgcaaatgctgaatagcttcccttttttattttagctcattcttg---cttttacctccatcaagttttttcccttagcaccatacatgtgtttgttagGAACATGCAAAAGGTGGAAAATGTATTGTTTTCACTCAAACAAAACGCGATGCTGATCGATTGGCATATGCTATGGCAAGAAACTTCAGATGTGAGGCTCMapped 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|254333821|gb|GR848739.1|GR848739EST: TTGCAACTGATTTGTATGTTAAAGCGGGAATTCTTGCTCCTCTAATAACG GAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGAT
genomic: TTGCAACTGATTTGTATGTTAAAGCGGGAATTCTTGCTCCTCTAATAACGgtatgccttc ... cctttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaggaaacttcttgctggatttttttttgtctcctaaagatatatcctttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
tcctaaa putative branch site (score: 2)
tcctttgtt putative PPT
atttttttttgtct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ggactaaaagatagtaaaccctatttttatttagaaaaactagttaaggaaacttcttgctggatttttttttgtctcctaaagatatatcctttgttagGAACATGCAAAAGGAGGAAAGTGCATTGTTTTCACTCAAACAAAACGTGATGCTGATCGATTATCATATACCATGGCAAGAAGTGTTAAATGTGAGGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - -aaaagata
- - - - - - - - - - - - - - - - agaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgctgga