Sequence
atgc intronic sequence ATGC exonic sequencegtattaacaaaatctatttgtaattccttatctcatattccatatgtgttgcctgcttattttatgtccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
Basic information
species | Glycine max |
transcript | GLYMA12G04820.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os03g12590.1 (Oryza sativa), 3'ss of exon 5
gtattaacaaaatctatttgtaattccttatctcatattccatatgtgttgcctg----cttattttatgtccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
| | | || ||| || | | |||| | || | | | | | | | ||| ||||||| || || || ||||||||||| || || || |||||||||||||||||||| || |||||||||||||||| ||| ||| | || || |
---------gtacacttctatagttctatacgaaaaaaaacataattcttttcggaagtcaaaaactgtacttattatatgcagGCAAATCCAGAAATCGTGAAAAGATGGAGCAACGAAGTGCAGGAAGCTGTTCAATCAAGATTTGCACTTGTGCAATTTCATGGCCTAGCTCTTCTTCACC
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 5
lower sequence: LOC_Os07g10150.1 (Oryza sativa), 3'ss of exon 5
-------------gtattaacaaaatctatttgtaattccttatctcat---------attccatatgtgttgcctgcttattttatgtccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
|| | | || | || |||| | ||| || | ||| || | || || | | | | || | ||||||| ||| || |||| ||||| ||||| ||||| |||||||| ||||| || || || || |||||||| |||||||||||||| ||| | || || |
gtatgtgcaaaacgtttagtctttgcctttatgcaattgcatattacagccagacccaaatccttacaaatgttttgtttgtatggt-tttattctgagcagACAAGTCCAGAAGTTGTGAAAAGGTGGAGCAATGAAGTTCAGGAGGCTGTACAGTCGAGAGCTGCTCTTGTTCAATTTCATGCCCTTGCTCTTCTTCACC
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G178618_T01 (Zea mays), 3'ss of exon 5
------------------------gtattaacaaaatctatttgtaattccttatctcatattccatatgtgttgcctgcttattttatgtccc--cccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
| | || |||| || | | | | |||| | | || || |||| || ||||| | ||| || |||||||||||||||| ||||| ||||| || ||||| || ||||| || ||||||||||||||||||||||| ||| | || || |
gtatgtcctgcagttatattttgtgctccagttggatatattgttactagttggtgcagctatagatatttttattatgttttccacatgtttgtattattggcagACGAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAATTTCATGCCCTTGCTCTTCTTCACC
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G036034_T01 (Zea mays), 3'ss of exon 5
-----------gtattaacaaaatctatttgtaattccttatctca----tattccatatgtgttgcctgcttattttatgtccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
| | || |||| || | || | || || | | | | | || | | | | | | || ||||||| ||| || |||||||||||||||| ||||| ||||| || ||||| || ||||| || ||||||||||| ||||||||||| ||| | || || |
gtatgtcctgtgctccacttggatatattgttactagtttgtggcagctttagttcttttttattatgttttccacatgtttgtactattggcagACAAGTCCGGAAGTTGTAAAAAGATGGAGCAATGAAGTTCAAGAGGCTGTGCAGTCAAGAGCTGCTCTTGTGCAGTTTCATGCCCTTGCTCTCCTTCACC
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 5
lower sequence: GRMZM2G012501_T03 (Zea mays), 3'ss of exon 4
gtattaaca-aaatctatttgtaattccttatctcatattccatatgtgttgcctgcttattttatg------tccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
||| || || || ||||| || | | ||||| | || | | ||| ||| | |||| || || | || ||| |||| || || ||||| ||||||||||| || || |||||||||||||| |||||||| || | ||||| || ||||||| ||| ||| | || || |
gtactagcataattctatgcatatataccgatctcttgtttaaggttggttaactgtatcttttgtgagtttgtctacactctacagGCAAACCCAGAAATTGTGAAAAGATGGAGCAACGAAGTTCAGGAAGCTGTGCAATCAAGAGCTCCACTTGTCCAGTTTCATGGCCTTGCTCTTCTTCACC
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 5
lower sequence: AT4G34450.1 (Arabidopsis thaliana), 3'ss of exon 4
-------gtattaacaaaatctatttg-taattccttatctcatattccatatgtgttgcctgcttattttatgtccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
|| || ||| ||||| | || | |||| ||| | |||| ||| | | | ||| | | || ||||||||| || || ||||| ||||||||||| ||||| ||||| |||| | ||||||| || |||| ||||| || || |||||||| |||||||| ||||
gtaccttttacacaccaaaactattaggtagcttctta------attgta-atgttatgcttatat-tcgtatattgctgttt-tcagACAAACCCAGAAATTGTTAAAAGATGGAGCAATGAAGTTCAAGAAGGTATTCAATCCAGATCAGCCCTTGTTCAGTTCCATGCCCTAGCTTTGCTCCATC
upper sequence: GLYMA12G04820.1 (Glycine max), 3'ss of exon 5
lower sequence: Vv03s0063g02450.t01 (Vitis vinifera), 3'ss of exon 5
--------------------gtattaacaaaatctatttgtaattccttatctcatattcc-atatgtgttgcctgcttattttatgtccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
| || | ||||||| || | ||| | || || | ||| | | || | | || ||||||| || ||||| || | ||| ||||||||||| || |||||||||||||||||||||||||| |||||||||||||||||||| ||| | |||||||
gtacaattgggttgtgtgtagattttttttattctatttata--tatttaaattatcctcttacatgctctaataatatgattattatttttttggat-agACAAACCCAGAGATAGTGAGAAGGTGGAGTAATGAAGTACAGGAAGCTGTTCAATCAAGGGCAGCACTTGTGCAATTTCATGCCCTAGCTCTCCTGCATCMapped 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|193573633|gb|FK530995.1|FK530995EST: CAGCCCTAGTTAGCGGTCATTCATATACTCCAG ACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTT
genomic: CAGCCCTAGTTAGCGG-CATTCATATACTCCAGgtattaacaa ... cccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTT
EST:
gi|193460558|gb|FK427999.1|FK427999EST: CAGCCCTAGTTAGCGGCATTCATATACTCCAG ACAAATCCCGAGATTTGTTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTG
genomic: CAGCCCTAGTTAGCGGCATTCATATACTCCAGgtattaacaa ... cccttatcagACAAATCCCGAGA-TTG-TAAAAAGATGGAGTAATGAGGTTCAGGAAGCTG
EST:
gi|193620509|gb|FK569101.1|FK569101EST: CAGCCCTAGTTAGCGGCATTCATATACTCCAG ACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTT
genomic: CAGCCCTAGTTAGCGGCATTCATATACTCCAGgtattaacaa ... cccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ccttatctcatattccatatgtgttgcctgcttattttatgtccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
ttttatgtcccccctt CT-rich tract
ttattttatgt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtattaacaaaatctatttgtaattccttatctcatattccatatgtgttgcctgcttattttatgtccccccttatcagACAAATCCCGAGATTGTAAAAAGATGGAGTAATGAGGTTCAGGAAGCTGTTCAATCAAGGGCAGCTCTTGTGCAATTTCATGCCCTGGCTTTGCTGCATC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC