Sequence
atgc intronic sequence ATGC exonic sequence...cttcttgattataaaatggatttttttttctctatatggagaggtttgttggatgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
Basic information
species | Glycine max |
transcript | GLYMA14G13750.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os06g43860.2 (Oryza sativa), 3'ss of exon 1
----cttcttgattataaaatggatttttttttctctatatggagaggtttgttgg---atgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
| | ||| |||| | | || ||| | | ||| | || | | || | | | ||| |||||||||| | | |||||| | || ||||| ||| | || ||||| ||||| |||||| | ||||| ||||| || || |||||||||||||||||||||||||| ||||| | || |
aagtcattttgtttatcaggtactcttctttgcttggaaatgacaatcttcctaaggcaattttttttacttaataaaaaaatgtttttttt-------tcttgcagACCCATTATGTATTGCTCCTTTGTTCGTTCAAGGAACAACTACAGCAACATGTGCGTGTTCATGCAATGGAAGCAGTAATGGCTTGCTGGGAACTTGAAC
upper sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os08g19650.1 (Oryza sativa), 3'ss of exon 1
cttcttgattataaaatggatttttttttct-ctatatggagaggtttgttggatgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
| || |||| | || | ||| | || || | |||||| | || | | || | | | ||| | | || ||||||| || ||| | | ||||| || ||||| || | |||||||||||||| || ||||| ||||||||||||||||| || ||||| | || |
-gttttatatatatagtgattctttcaacatacttgatcactacatttgttttagagtttatcacttcatgttagtaacctgtagttgtttcttttcttagACGCACTACGTCTTGCTATTATGTTCGTTTAAAGAGCAGCTACAGCAGCATGTCCGTGTTCATGCTATGGAAGCAGTAATGGCATGCTGGGAACTTGAAC
upper sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os02g08544.2 (Oryza sativa), 3'ss of exon 1
cttcttgattataaaatggatttttttttctctatatggagaggtttgt-tggatgtggtacagttacggttttaatg---ttttttatggttggat--gttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
||| | | | || | | | ||| | | || | || | | | | | || | || | | || || | |||||| | || ||||| ||| | || || || ||||| |||||| | ||||||||||| || || ||||||||||||||||| |||| || ||||| | || |
-----tgacccctgtgtt-actccttatcttggaaatgaacatgtcattgtgtttttcacatggcagcccttcttgtggactctaacatacttctcttaattgcagACACATTATGTGTTGCTTCTTTGCTCATTCAAGGAACAACTTCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTGATGGGGTGCTGGGAACTTGAAC
upper sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G055243_T01 (Zea mays), 3'ss of exon 1
---------cttcttgattataaaatggatttttttttctctatatggagaggtttgttggatgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
| | ||| | | | || || | ||| | | | || || |||| | || ||| | | | | || | | ||| | || ||||| ||| | |||||||| ||||| |||||| | ||||||||||| || || ||||||||||||||||| |||||||||||||| | || |
ataattaatcattttgtggcaagagcaggttgttatcattctctgttttttccctctttcga-atggttcta----aattctaacctgtctcgtttttcg----tccagACACATTATGTGTTGCTCCTCTGTTCATTCAAGGAACAACTCCAGCAGCATGTGCGTGTTCATGCAATGGAAGCAGTCATGGCTTGTTGGGAGCTCGAAC
upper sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G433591_T02 (Zea mays), 3'ss of exon 2
--cttcttgattataaaatggatttttttttctctatatggagaggttt-gttggatgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
|| | | | | || || | || | ||| | | | | | || |||| | || || || | |||||| |||||||||| ||| | || || || ||||| ||||| ||||||||||||| || || ||||||||||||||||| |||| ||| ||||| | || |
tctttgtctagggttctgtacatagttaacatcttgcatcatctgtttttgccaggccttcttgttcccagattctaatatattcc-tgtttt--tattgcagACGCACTATGTATTGCTCCTTTGCTCATTCAAGGAACAGCTGCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAAC
upper sequence: GLYMA14G13750.2 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G370332_T01 (Zea mays), 3'ss of exon 1
cttcttgattataaaatggatttttttttctctatatggagaggtttg-ttggatgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
|| | | || | || || | || | |||| | | | | | || |||| | | || || | || ||| |||||||||| ||| | || || || ||||| |||||| | ||||||||||| || || ||||||||||||||||| |||| ||| ||||| | || |
tttgtctaggattccgtacatagttaacatcttgcatcatctgttttggccaggtattcctgttctcagattctaatatgtcac-tgttttattattacagACGCACTATGTATTGCTCCTTTGCTCATTCAAGGAACAACTCCAGCAGCATGTACGTGTTCATGCAATGGAAGCAGTGATGGGTTGCTGGGAGCTTGAACMapped 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|209728697|gb|BW655404.1|BW655404EST: TCGGACACA-CAACATCGTCGCCGATGACAAAGAACTCGATCAGTTCATG TCGCACTATGTTTTGTTGCTCTGTTCCTTCAA-GAACA-TTGCAGCAGCAT
genomic: TCGGACACAACAACATCGTCGCCGATGACAAAGAACTCGATCAGTTCATGgtatatacaa ... gatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCAT
EST:
gi|13480317|gb|BG509660.1|BG509660EST: TCGGACACAACAACATCGTCGCCGATGACAAAGAACTCGATCAGTTCATG TCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCAT
genomic: TCGGACACAACAACATCGTCGCCGATGACAAAGAACTCGATCAGTTCATGgtatatacaa ... gatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttggatgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
ttttaat putative branch site (score: 3)
ttttaatgttttttat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
cttcttgattataaaatggatttttttttctctatatggagaggtttgttggatgtggtacagttacggttttaatgttttttatggttggatgttgcagTCGCACTATGTTTTGTTGCTCTGTTCCTTCAAAGAACAATTGCAGCAGCATGTCCGGGTCCATGCAATGGAAGCAGTAATGGCTTGTTGGGATATAGAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG