Sequence
atgc intronic sequence ATGC exonic sequence...tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
Basic information
species | Glycine max |
transcript | GLYMA14G11220.1 |
intron # | 24 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os02g53720.2 (Oryza sativa), 3'ss of exon 1
--------------------------------------------------------------------------------------------------------------tttgtagtgtttcatttattataatggtattttatt-atcattctgcctatt--taaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
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gtgatgcatctgcagaggtcccagtccattgattttacccatcaatttcggtagctgtttggcaagtgtcctctcgtcacactcaaccttgcaaatgatctattacatgtctcagactattgcatatgttcgccctctacttgatagatgcatttggttgttaacagagtgatattattattttcctgtgatagATATCCATGC-ACTACCATCAAGTAATGTTCCTCCAAAGCTTGTAATCCTTCACATGAACATGGCATTCCTTGTGTACGAAGATATAATGAGGATGACTGA------------------
upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: LOC_Os06g10230.1 (Oryza sativa), 3'ss of exon 24
----------------------------------------------------------------tttg--tagtgtttcatttatta-taatggtattttattatcattctgcctat---ttaaacttaagttgacaagttactgactgcataa-gctatgttattg-----acagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
|| | || | | | | | | | || |||||| | | | || | | | | | | ||| | | || | | ||| | | ||| ||||| | || || ||||| || || ||||||||||| | | || | ||| || || ||||| |||| ||||||||||||||| |||||||||||
gtaatgcatctgcaaggagttttgctcaacaaatcaactcatttctctcctgccaagttcaatattaggatactatcttgtccagcaattattgtatttagtcaattgtttgtttttacctgataactgggttaatggtagagcaacactaaagcgctgtatatttgctgtcacagTGAGCAATGTTCCCCCCAAGCTGGTTATCCTTCATATGAACCTTTCCCTTCTTGTATACGAGGATATAATGACGATGACTGAAAACCTGAGTGAGAAGTA
upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM5G809695_T03 (Zea mays), 3'ss of exon 23
----tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
||| ||| |||| || | | || | | | | || | |||| | | || || || | || |||| | || || ||||| ||||| ||||||||||| ||||| || ||||| | ||| ||||| |||||||||||||| ||| | |||||||| ||
attcaactcagtattttattttgta-agttataactggtcgctaatagttgatgctagaacggcattgatatcatgttgttgatat---tcattctgtttgcagTGAGCAATGGTCCACCCAAGCTGGTGATCCTTCATATGAACATGGCTCTTCATGTCTTTGATGATATAATGAGGATGACTGAGAACTTGAGTGAGAAATA
upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: GRMZM2G463904_T03 (Zea mays), 3'ss of exon 24
tttgtagtgtttcatttat-tataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgc-ataagctatgttatt--gacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
|| ||| ||| | ||| || | |||| || | | | | || | || | | | | |||| | | | || | || || | | ||| ||||| ||||| || || ||||| ||||| || |||| ||||| ||||| |||||||||||||||||| | || || ||
cctg-agttcagaattcaaatatgctgacaacttatgtgacttgtacggctgttaattaaataatattactaatgcactgtgacagataaccttgcttcagCATCAAACAACATTCATCCCAAGCTTGTGATCCTCCACATGAACATGGCCCTCTATGTATATGATGATATAATGAGGATGACTGAAAACTTGAGCGAAAA---
upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: AT2G26330.1 (Arabidopsis thaliana), 3'ss of exon 24
tttgtagtgtttcatttattata-atggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
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-------------gtctactctccaaaccactttacgaatgttcttc--acctacaatgtaatccaatagttaatccttaaatttcct--ggtgacatcagTAACTTATTCGACACCGAAGCTCGTCATCCTTCATATGAACATGGCACTCCACGTTTACGAGGATATCATGAGAATGACAGAGAATCTAAGTGAGAAGTA
upper sequence: GLYMA14G11220.2 (Glycine max), 3'ss of exon 24
lower sequence: Vv04s0008g01970.t01 (Vitis vinifera), 3'ss of exon 24
-----tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
| |||| || || |||| | | | | | ||| ||| | ||| || |||||| | | | |||| ||| || | | | ||||||| | ||| | || ||||| ||||| ||||| |||||||||||||| |||||||| || ||||||||||| ||||| |||||| | |||||||||||
ttatatctgtatcccttaatatattttgaaa--aatgtgttactattttcccttttgaaactt---ctctccatctactaactaatgtagtttgctaaacaacagTTACATACTCAACACCGAAGCTGGTGATCCTTCACATGAATATGGCACTGCATGTGTACGAGGATATCATGAGAATGACGGAAAACTTGAGTGAGAAGTAMapped 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|7692537|gb|AW760640.1|AW760640EST: CCGACCACACAGCCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAA TTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC
genomic: CCGACCACACAGCCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAAgtacttatct ... ttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC
EST:
gi|27424345|gb|CA935865.1|CA935865EST: CCGACCACACAGCCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAA TTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC
genomic: CCGACCACACAGCCCCTCTCCTTTTCCTGATGGATCATTTGACAAACCAAgtacttatct ... ttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
tactgac putative branch site (score: 1)
ttaaacttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tttgtagtgtttcatttattataatggtattttattatcattctgcctatttaaacttaagttgacaagttactgactgcataagctatgttattgacagTTAATTTCTCCCCTCCAAAGCTAGTGATTCTTCATATGAATATGGCACTACATGTGTATGAAGATATCATGAGGATGACTGAAAACCTAAGTGAGAAGTA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT