Sequence
atgc intronic sequence ATGC exonic sequence...ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
Basic information
species | Glycine max |
transcript | GLYMA07G05390.2 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os04g59040.1 (Oryza sativa), 3'ss of exon 4
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtcta---tcattatattcttcttacctt--ctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
|| || | || | | ||| || | | ||| | | | || ||| | |||| ||| || | || | | || | | | ||||| || || || | |||||||||||||| ||||| ||||| ||||||||||| ||||| || || |||||||||||||||||||| ||||| |||| |
-----ctgtgttgtattatttgataggtctgcatttgtaagctgtaggagtttattcttgtcaaagaatattacatttttgtaactgtgcttcataatttgacagGTCGACCGTGTCCTATACTCATCAGTTGTGTATCCCCATAATTATGGTTTCATTCCAAGGACACTTTGTGAAGACAATGATCCAATGGATGTTCTGGTCC
upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os01g64670.1 (Oryza sativa), 3'ss of exon 3
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
|| | ||||| || | || | | | ||| || || | | || | | | | || || || |||||||||||||| |||||||| ||||| ||||| || || ||||| || |||||||| |||| || || |||||||| |||||||| ||||| | || |
-----gtctgtaatcaaacactgtatttatacactcacg--tcagggaccatatgctctgtggaacttttttaccatttgggctc----ttgttgtacagGTTGATCGGGTCTTGTACTCGTCAGTGGTTTACCCCCACAACTACGGCTTCATCCCTCGAACGCTCTGCGAAGACAACGATCCAATGGATGTTCTAGTGC
upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G104918_T03 (Zea mays), 3'ss of exon 4
ttcttgtggattctcaaatcttgacccttcgcaattctg-acttgtgga-tgccattactcg-tctatcattatattcttcttaccttc-taattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
|||| | | | | | ||||| || || | || || | | | | || | | |||| ||||| | | | | ||||||||||| || | |||||||||||||| || ||||| || ||||||||||| ||||| ||||| |||||||||||||| ||||| ||||| ||||| |
----tgtgttacataatttgtcaggatgattgagttctgtgctgatgaaatgtaatagtttaatttgtttttctttctttctaacctttgctacaatttgacagGTTGATCGAGTCCTTTACTCATCAGTTGTATACCCTCACAATTATGGTTTCATTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTGGTCC
upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G061928_T02 (Zea mays), 3'ss of exon 4
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtgga--tgccattactcg-tctatcattatattcttcttacct-tctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
||| | || || | | | || | |||| || || || || | | | | || | | |||| || | | | | | | |||||||||| || |||||||||||||||| || ||||| || ||||||||| | ||||| ||||| |||||||||||||| ||||| ||||| || || |
-tctgttacataatc---tgtcaggctgattcagtcctgaactgatgaaatgtaatggtttaatttgactttctttcgttctgacatgtgctacaatttgatagGTTGATCGAGTCCTGTACTCATCAGTTGTATACCCTCACAATTATGGTTTCGTTCCAAGGACTCTTTGTGAAGACAATGACCCAATGGATGTGTTAGTCC
upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: AT2G46860.1 (Arabidopsis thaliana), 3'ss of exon 3
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
| || |||| ||| ||||| | || || | | || | | | || || | || || ||||||||| ||| | |||||||| || ||||||||||| || || || || ||||||||| | || ||||||||||||| ||||| |||||||| | || |
-----------------gtaatgtgacttcccaa----agattgtgatcttcttttctt-ttaactgttctgatgga-tgacattgaatttgatc-tcagGTTGACCGGATCTTGTACTCCTCCGTTGTTTATCCACACAATTACGGATTCATCCCACGGACATTGTGTGAAGACAACGATCCTCTTGATGTCCTTGTCC
upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: AT1G01050.1 (Arabidopsis thaliana), 3'ss of exon 4
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
| | || || | || | | | || ||| || | | || | || | | | |||||||||||| || | |||||||||||||| || ||||| ||||||||||| | || | || |||||||||||||||| || ||||||||||| ||
------------gttagatgagaacaaagtttatttttta--tatgaatggttttcttatagcaaaatcaatctcaacaagtttgaattctctcattcagGTTGATCGTATTCTCTACTCATCAGTTGTGTACCCTCACAACTATGGTTTTGTTCCTCGCACATTGTGTGAAGACAATGACCCCATTGATGTCTTAGTCA
upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv02s0025g02980.t01 (Vitis vinifera), 3'ss of exon 3
-----------------------------------------------------------------------ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaa--ttaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
| | ||| | | || |||| || | | | || ||||| | | | || || || || || | ||| | |||| ||||| || || || || || ||||| || || ||||||||||||||||| ||||| || | || || |||||||||||||||||| | ||||| || | |
gtaagactgaaccctgaagtgctttaatttccagacatttttccacatgatttggatatttgagcaccaaatcaccattgatggagatctgttttttcttccattttgttatgtatgcatgccttcatatg---atgggaatgttttttctattgtttaacatcaatgcccagGTCGACCGTGTCTTATATTCATCTGTGGTGTATCCTCATAACTATGGATTCATTCCCCGTACCCTATGTGAAGACAATGATCCACTGGATGTTTTAATCC
upper sequence: GLYMA07G05390.1 (Glycine max), 3'ss of exon 4
lower sequence: PP1S46_53V6.1 (Physcomitrella patens), 3'ss of exon 5
-----ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccatta-ctcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
| ||| | || ||| || | ||| | | || || || | || | | | | ||| | | | |||||||||||| | ||||||||||||||||| ||||| || || ||||| ||||| ||| | ||||| ||||| || | ||||| |||||||| | ||
gtacgtcattgccagtgactaactctaaacgatcttgtcttcatatcttcacgagctgttggcttggct-caaccaccgctccttaatcttaacctcatttttcagGTTGATCGTATCTTGTACTCATCAGTTGTCTATCCACACAATTATGGGTTCATTCCACGTACTCTTTGTGAGGATGAGGATCCCATTGATGTTCTCGTCAMapped 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|17400209|gb|BM176991.1|BM176991EST: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG GTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTC
EST:
gi|48574801|gb|CO036084.1|CO036084EST: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAG GTTGATCGGGTTTTGTAC
genomic: AGGGAAGCAAGGTCAAATACGAACTTGACAAAAAGACTGGATTAATTAAGgtatgaacca ... taatggtcagGTTGATCGGGTTTTGTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
tatcattatattctt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
ttcttgtggattctcaaatcttgacccttcgcaattctgacttgtggatgccattactcgtctatcattatattcttcttaccttctaattaatggtcagGTTGATCGGGTTTTGTACTCATCAGTTGTTTATCCTCATAACTATGGTTTCATCCCAAGAACTCTGTGTGAAGACAATGATCCAATTGATGTCTTGGTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
-tcttgtg
- - - - - - - - - - ttgaccc
- - - - - - - - - - - - - - - - - ttctgac
- - - - - - - - - - - - - - - - - - - - - - -ggatgcc