Sequence
atgc intronic sequence ATGC exonic sequence...taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
Basic information
species | Glycine max |
transcript | GLYMA19G34890.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 4
------------taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagt-----attttaacactatattcctccacaattgctcttt--cagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
| | | ||| ||| |||| || | | ||||||| | | | | | | | | | || | | | | | | | | || | | |||||||| || || | | || |||| ||||||| ||||| | | | |||||||||||||| ||||| |||||||| ||||||||||||||| |||
gtaagtttgttctttagaatctttcaccaataatttcttatcacaaacatgatacatatttaaatgttgggctttttcaaacttcattattgtgattcatcttttctactatctggcagATGCTAAAGTTCAAAGATAACAATATTAACAATGAGGGAATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G067764_T02 (Zea mays), 3'ss of exon 4
taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
||| | | | ||| | | | | | ||||| | ||| || || | |||||||| ||||| | || |||||||||||| || | | | | |||||||||||||| ||||| |||||||| ||||||||||||||| |||
-----------------gtaagccttttgtcttgattct----tttgtaagttgccctgaaattctttaatctaacccatctctactgtt----tggcagATGCTAAATTTCAAGGATAACAATATAAACAATGATGGGATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTTGGAGGATATCTTCTTT
upper sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G575696_T01 (Zea mays), 3'ss of exon 2
taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
||| | | || || | || | || | | ||||| | || ||| || ||| | ||||| || ||||| | | || |||||||||||| ||| | | | |||||||||||||| ||||| |||||||| || |||||||| ||| |||
-----------------gtaagccttttgtcttgactcctttgtaagtttccca---gaaattcttttatctgaccat--ctctactatt----tgccagATTCTAAATTTCAAAGATAACAATATAAACAATGAGGGGATGCTTCGTATAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTCGGAGGATACCTTCTTT
upper sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G433989_T01 (Zea mays), 3'ss of exon 1
taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
||| | | || || | || ||| | | ||||| | || ||| || ||| | |||||||| ||||| | | || |||||||||||| ||| | | | |||||||||||||| ||||| |||||||| || |||||||| ||| |||
-----------------gtaagccttttgtcttgactcctttgtaagtttccc---tgaaattcttttatctgaccat--ctctactatt----tgccagATGCTAAATTTCAAAGATAACAATATAAACAATGAGGGGATGCTTCATACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTCGGAGGATACCTTCTTT
upper sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 4
lower sequence: GRMZM2G107629_T03 (Zea mays), 3'ss of exon 5
taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
||| | | || || | || ||| | | ||||| | || ||| || ||| | |||||||| ||||| | | || |||||||||||| ||| | | | | |||||||||||||| ||||| |||||||| || |||||||| ||| |||
-----------------gtaagccttttgtcttgactcctttgtaagtttccc---tgaaattcttttatctgaccat--ctctactatt----tggcagATGCTAAATTTCAAAGATAACAATATAAACAATGAGGGGATGCTTCGTACAGTTCTTGATGTTGGTTGTGGAGTTGCTAGTTTCGGAGGATACCTTCTTT
upper sequence: GLYMA19G34890.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 4
taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
| | | | ||| | | | ||||| || | | || || | | | | | |||| | | |||||| |||||||||||||||| ||||||| | | |||||||||||||| | ||| | ||||||||||||||||||| ||||||||||||||||| |||||| ||
------gtaaggcagttactagatc-ttatgtgga-atagaggtgtgtgtccatcttca---tttactgatacta---ttcatggaaattgc------agATGCTTAATTTTCCGAACAATGTTTTGAACAATGGGGGAAGGCTGAGGACATTTCTTGATGTTGGCTGTGGTGTTGCTAGCTTTGGAGGTTATCTTCTTGMapped 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|33390342|gb|CA853537.1|CA853537EST: GAACCCACTTCCATTATGGTGCTGGTAAATACATTGCTTCAATTGCTAAT ATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCT
genomic: GAACCCACTTCCATTATGGTGCTGGTAAATACATTGCTTCAATTGCTAATgtaagcctca ... gctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCT
EST:
gi|33390338|gb|CA853533.1|CA853533EST: GAACCCACTTCCATTATGGTGCTGGTAAATACATTGCTTCAATTGCTAAT ATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCT
genomic: GAACCCACTTCCATTATGGTGCTGGTAAATACATTGCTTCAATTGCTAATgtaagcctca ... gctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
ttttaac putative branch site (score: 2)
ttgctctttc putative PPT
tattttaacactatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
taaaacacattttacccataaaatcatcacccaaacatagaagtttctcacctaattgagagtattttaacactatattcctccacaattgctctttcagATGCTTAATTTTCCAAACAATGATATAAACAATGGGGGAAGAGTCAGGTCTGTTCTTGATGTTGGCTGTGGGGTTGCTAGCTTTGGAGGATATCTTATTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- -aacacat
- - - - - - -acccata
- - - - - - - - - - - - - - - ccaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttcctcc