Sequence
atgc intronic sequence ATGC exonic sequencegtatgcctttttgcaatattatgcagcgagatgttaactgcgactcatgatgtgatcttgttcatttatacttcttactttgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 6
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 3'ss of exon 6
gtatgcct-ttttgcaatat--tatgcagcgagatgttaactgcgac----------tcatgatgtgatcttgttcatttatacttcttactttgaa-ctgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
| || ||| |||| | ||||||| | ||||||| | | | |||| ||||| |||| || | || |||| | |||| | ||||||||||||||||||||||| |||||||| |||||||| ||||| |||||||||||||| ||||||||||||||||||||||||||||||||||||||||
----gtctgtttcacaatctcttatgcagtg-gatgttattcacaatatatggctttttatgaggtgat-ttgtgcactaatggttctaaaactgaaacaacagATATGGAGTTTGGGTTCTCCGGATCCAAATTTCACACTCGATGGACATCAAAAGGGTGTGAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 6
lower sequence: Vv11s0016g04180.t01 (Vitis vinifera), 3'ss of exon 6
----------gtatgcctttttgcaatattatgcagcgagatgttaactgcgactcatgatgtgatcttgttcatttatacttcttactttgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
|| |||| || || | | || | || | ||| || | | || | | | ||| | | | ||||| |||| | | || || || || ||||| || || | |||| || || || || ||||||||||| ||||||||||||||||||| ||| || |
tatactttaagtcgctgttttggcggctttttcaatacagtttttctcctttacttataaaaaaaaaaagtcctaatgttgatctggcgtcctgttccagATTTGGAATCTCGGCTCCCCTGACCCAAATTTTACTTTGGATGACCACATGAAAGGGGTAAACTGTGTTGATTACTTCACTGGTGGTGACAAGCCATACT
upper sequence: GRMZM2G000645_T03 (Zea mays), 3'ss of exon 6
lower sequence: PP1S243_63V6.1 (Physcomitrella patens), 3'ss of exon 6
--------------------------------------------------------------------------------------gtatgcctttttgcaatat---tatgcagcgagatgtt--aactgcgactcatgatgtgatcttgttcatttatacttcttactttgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
| ||| ||| || | | || | |||| || | || || | ||| ||| | || | ||||| | ||||||||| |||||||| ||||| || ||||| || || || | ||||| |||||||||||||| || || |||||||||||||||||| | || |||
gtgagatattatgtgcttcgatgttcttctattggcattatgtacgtaaagaaattctatgaaaaaaaaaggaagagttttaatccactcgacttgttgtggaatgcttttttagggtagtgttctaaacgtatatcgccatattgagttgatcagatgagctctgt-ctttg---tatagATATGGAACTTGGGTTCACCAGAGCCCAACTTTACCCTCGAGGCTCATCAGAAGGGTGTCAACTGCGTGGAATACTTCACTGGTGGTGACCGACCACATTMapped 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|26457397|gb|CA828980.1|CA828980EST: GCACTACAAAG ATATGGAG-TTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAA
genomic: GCACTACAAAGgtatgccttt ... tgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAA
EST:
gi|32931674|gb|CF036486.1|CF036486EST: CAAAGGATATTAACACCTTTGCAAGTGCATCCCTTGACCGCACTACAAAG ATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAA
genomic: CAAAGGATATTAACACCTTTGCAAGTGCATCCCTTGACCGCACTACAAAGgtatgccttt ... tgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aactgcgactcatgatgtgatcttgttcatttatacttcttactttgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
ttcttac putative branch site (score: 2)
cttcttacttt CT-rich tract
atttatacttctta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgcctttttgcaatattatgcagcgagatgttaactgcgactcatgatgtgatcttgttcatttatacttcttactttgaactgcagATATGGAGTTTGGGTTCTCCAGATCCAAACTTCACACTTGATGGGCATCAAAAGGGTGTCAACTGTGTTGACTACTTCACTGGTGGTGACAGGCCCTATT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG