Sequence
atgc intronic sequence ATGC exonic sequence...gaagcattctaaatcaaattatatatatagtttacttttgaatttcatatttttacaatataagtacatatttaacttttggaagcaatattgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG
Basic information
species | Glycine max |
transcript | GLYMA10G35490.1 |
intron # | 14 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 12
lower sequence: LOC_Os07g26610.1 (Oryza sativa), 3'ss of exon 13
gaagcattctaaatcaaattatata-tatagtttacttttgaattt--catatttttacaatataagtaca-tatttaacttttggaagcaatattgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG
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--gttagtttgtactga-ttgtataattcagattgtcttgaaatttgttctatttcacctggctgaataaaatgtaagtcattcctggtcaatctttc----agAATACTATTGGTGAGGAGTCACATTTAGCTATGGAAACAAGTGGCCATGGAGCACTGAAAGAGAATCACTGGCTCGATGATGGTGCATATCTTATG
upper sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 12
lower sequence: GRMZM2G069676_T02 (Zea mays), 3'ss of exon 12
gaagcattctaaatcaaattatatatatagtttac---ttttgaatttcatatttttacaatat---aagtacatatttaacttttggaagcaatattgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG
| ||| | ||| | ||| | |||| || || | || ||| | ||| | | | ||| ||| | | ||||| |||||||| ||||||||||||||||| || ||||| ||||| |||||||| || || || || || |||||||||||||| |||||||| |||
------tatgtaattgagttagtccctgaatttccatattttaaaatttccgtccctaaaatttttcaagcagtaggatgagatttagaatatggaaaattttcagAACTCTATTGGTGAGGAGTCACATTTGGCCATGGAAACAAGTGGGCATGGAGCGCTGAAAGAGAACCACTGGCTTGATGATGGAGCATACCTTATG
upper sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 12
lower sequence: AT5G17530.3 (Arabidopsis thaliana), 3'ss of exon 13
gaagcattctaaatcaaattatatatatagtttacttttgaatttcatatttttacaatataagtacatatttaacttttggaagcaatattgc--tgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG
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gttagatagagaaaccatacattctggcaggaaaagcttactccgccttatggaccattgataattcttatctgaaa--tagaagttgtgatgtgatggcagAACTCGGTTGGGGAAGAATCACATCTGGCTATAGAAACCAGTGGTCATGGAGCTCTAAAGGAAAACCATTGGCTCGACGATGGGGCCTATCTCATG
upper sequence: GLYMA10G35490.2 (Glycine max), 3'ss of exon 12
lower sequence: Vv13s0019g04370.t01 (Vitis vinifera), 3'ss of exon 13
---gaagcattctaaatcaaattatatatatagtttacttttgaatttcatatttttacaatataagtacatatttaacttttggaagcaatattgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG
|| || | | | | | | | || || |||| ||| || | || | || ||||||| | || ||| |||||||||||||||| |||| |||||||||||| |||| ||||| |||||||| ||||||||||||||||| ||||| ||||||||||||||||||||||| |||
tataaacaatcttcttccttgtcacactttggttactattctgcattttgggtttccactgc-tgagaatat-tttaactga-agcagtaatgttgctgacagAATTCTGTTGGTGAGGAGTCACATCTGGCTATTGAGACTAGTGGCCATGGAGCTCTCAAGGAGAATCACTGGCTTGATGATGGTGCATACCTCATGMapped 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|58023217|gb|CX709958.1|CX709958EST: ATCGGTTCAAAAGAGGTTACAAAAATGTGATTGATGAAGCTATTCGTTTG AATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGA
genomic: ATCGGTTCAAAAGAGGTTACAAAAATGTGATTGATGAAGCTATTCGTTTGgtatgatgag ... ttgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGA
EST:
gi|57575221|gb|CX548196.1|CX548196EST: ATCGGTTCAAAAGAGGTTACAAAAATGTGATTGATGAAGCTATTCGTTTG AATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGA
genomic: ATCGGTTCAAAAGAGGTTACAAAAATGTGATTGATGAAGCTATTCGTTTGgtatgatgag ... ttgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.catatttttacaatataagtacatatttaacttttggaagcaatattgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG
atttaac putative branch site (score: 3)
ttttacaatataagta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gaagcattctaaatcaaattatatatatagtttacttttgaatttcatatttttacaatataagtacatatttaacttttggaagcaatattgctgacagAATTCTATTGGCGAGGAGTCACATTTGGCAATTGAAACTAGTGGACATGGAGCTCTCAAGGAAAATCATTGGCTTGATGATGGTGCATACCTAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA