Sequence
atgc intronic sequence ATGC exonic sequence...atgtgcttttcgatcctcggcttatgtttttatttttctacatttatgtgagatttattttacatgcaatcaactgacttctattttttccccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
Basic information
species | Glycine max |
transcript | GLYMA13G29010.1 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 6
lower sequence: LOC_Os03g57290.1 (Oryza sativa), 3'ss of exon 6
----atgtgcttt--tcgatcctcggcttatgtttttatttttctacatttatgtgagatttattttacatgcaatcaactgacttctattttttccccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
||| ||| | ||| |||| | ||||| | | || | | ||||||||| |||| || | | ||||| | ||||| |||||||||||||||||||| |||||| | |||||||||||||| || || || || || || || ||||||||| ||||||| | | | |||||||
ttttttgtacttaagtagatgtgtaatttat-cctgcattttctttctttgtactatgttttattttatgaaagatcagctcaagcccttttttcc-----aacagAATCGACCTGCTGAATTGATTGCGAAGTTTCTTGATGAGAAACTTCGAGCTGGAAATAAAGGTACCTCCGAAGAAGAGCTGGAGGGAATATTGGATAAAG
upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 6
lower sequence: AC155496.2_FGT009 (Zea mays), 3'ss of exon 6
atgtgcttttcgatcctcggcttatgtttttatttttctacatttatgtgagattta-ttttacatg---caatcaactgacttctattttttccccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
||| || || | | || || || | || || | | ||| || || ||| | |||| | | | | | | |||||||||||||| ||||||||||| |||||| | |||||||||||||| || || || || || || || ||||||||| ||||||||| |||||||||||
-tgt-ctgttgtagctaaactttccattcttggtagagtagtttagttttttttttggttctatatgttcctgtcaaataa--tgggtcccatgcttacaacagAACCGACCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCTGGCAATAAAGGGACATCGGAAGAAGAGCTGGAGGGTATACTTGATAAAG
upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 6
lower sequence: GRMZM2G704093_T02 (Zea mays), 3'ss of exon 6
atgtgcttttcgatcctcggcttatgtttttatttttctacatttatgtgagatttattttacatgca-atcaactgac---ttctattttttccccttgcca---gAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
|| | | || | | | | || || ||| | | ||| ||| || || | | |||| | | | | || ||| | || || |||||| ||||| ||||||||||| |||||| | |||||||||||||| || || || || || || |||||||||||| ||||||| | |||||||||||
-------ttcttagaaatgcctgagggctgtcttactccacacatgtcagagtttttttatatgttcttgtcaagtaatgggtcccatgtttgtttcatgtcaacagAACCGTCCTGCGGAATTGATTGCAAAGTTTCTTGATGAGAAACTTCGAGCTGGCAATAAAGGGACATCAGAAGAAGAGCTGGAGGGCATACTTGATAAAG
upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 6
lower sequence: AT5G46210.1 (Arabidopsis thaliana), 3'ss of exon 6
atgtgcttttcgatcctcggcttatgtttttatttttc-tacatttatgtgagatttattttacatgcaatcaactgacttctattttttccccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
||| | || | | | | ||| || ||| | || | | || | || || | | || | | || | ||||||| || ||||| | ||||||||||||||||| |||||||| ||||| || || ||||| ||||| |||||||| |||||| || ||||| ||||
tagtgttgtttgctaatatatatcactttggataccaaatactctgatttagcaagcatcccaaataatatacatcttatgctgataatcttttttac-agAACCGGCCAGCTGAGCTTATTGCCAAGTTTTTGGACGAGAAACTCCGTGCTGGGAATAAGGGTACTTCTGAAGAAGAATTGGAGAGTGTTCTTGAAAAAG
upper sequence: GLYMA13G29010.1 (Glycine max), 3'ss of exon 6
lower sequence: Vv10s0003g03710.t01 (Vitis vinifera), 3'ss of exon 6
atgtgcttttcgatcctcggcttatgtttttatttttct--acatttatgtgagattta--ttttacatgcaatcaact--gacttctattttttccccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
| || | | | | | || | || | ||||| | | || ||| ||| | | |||| || | | | | | || |||||||||||||||| | ||||| |||||| ||||||||||||||||||| || |||||||| || || ||||| |||||||||||||||||||||||||
------tgtttaaatttggattatttcttatggttcattgaacattactttcagtattagcccttaaaaattttaaactaagagtgtcttgtgcttcttttaatagAACCGACCTGCTGAGCTTATTGCAAAGTTTCTGGATGAGAAACTTCGTGCTGGGAACAAGGGTACATCTGAAGAGGAGTTGGAGGGTACACTTGATAAAGMapped 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|7478748|gb|AW666390.1|AW666390EST: TCTGTAACACCATCAAAGATTCGTTTGAGCATCTCATCAATCTTCGTCAG AACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCA
genomic: TCTGTAACACCATCAAAGATTCGTTTGAGCATCTCATCAATCTTCGTCAGgtacttctca ... cccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtgagatttattttacatgcaatcaactgacttctattttttccccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
aactgac putative branch site (score: 2)
cttctattttttcccc CT-rich tract
agatttattttacat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
atgtgcttttcgatcctcggcttatgtttttatttttctacatttatgtgagatttattttacatgcaatcaactgacttctattttttccccttgccagAACCGACCTGCTGAATTGATTGCCAAGTTTTTGGATGAGAAACTTCGTGCAGGTAACAAGGGCACTTCAGAAGAAGAGTTGGAGGGTACACTTGATAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- -tgctttt
- - - - - - - - - -gcttatg
- - - - - - - - - - - - - - - - - - -ctacatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatgca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caactga