Sequence
atgc intronic sequence ATGC exonic sequenceGGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatatcttcctctaaactcatactacttacttttctcttgggttgttatctaaggctatgcatgtttgcaacatgtaatgacgtgatgagaaactaacccgagatccaatttcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G70730.1 |
intron # | 4 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: LOC_Os03g50480.1 (Oryza sativa), 5'ss of exon 4
GGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatatcttcctctaaactcatactacttacttttctcttgggttgttatctaaggctatgcatgtttgcaacatgtaatgacgtgatgagaaactaacccgag-atccaatttcag
||| || |||||||| || |||||||| |||||||| |||||||| || | || ||||| || ||||| ||| |||| ||||||||||| || || ||||| |||| | || | || | | ||| || | | || || || | ||| | | || | ||| || | | | | | | | ||| || ||
GGCTGCCGCTAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGCCTCATGTCTACTCCAGCTGTATCTGCTGTTATCCGTGAAAGAGTTGGTGCAGATgtaagatttattttacaaagatta-actttttgcagtgtgactg--ttagtactcactgcttattttctctgtgttaacaaattaccttactggtgctttatcaaatcatcaaaaaatag
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G109383_T01 (Zea mays), 5'ss of exon 4
GGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatatcttcctctaaactcatactacttacttttctcttgggttgttatctaaggctatgcatgtttgcaacatgtaatgacgtgatgagaaactaacccgagatccaatttcag
||| || || ||||| || |||||||| |||||||| ||||||||||| | || |||||||| ||||| ||| | || ||||||||||| || || ||||| || | || || || | | | ||| | | || | || || | || | || | | || || ||| | | | | ||
GGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAAGAGTTGGTGCAGATgtaagttggatttctaataaaggacattctttagcaatatgaacatttacttgttactcctttacaccgtc-taataaattat-acctgactattggtttataaacacatggacaatag
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 4
GGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatatcttcctctaaactcatactacttacttttctcttgggttgttatctaaggctatgca-tgtttgcaacatgtaatgacgtgatgagaaactaacccgagatccaatttcag
||| || || ||||| || |||||||| |||||||| ||||||||||| | || |||||||| ||||| ||| | || ||||||||| | || || ||||| || | ||| | | | | | ||| | | || | || || | | ||| | || |||| || || | ||| | || | ||
GGCTGCTGCCAATGGAGTAAGACGTGTTTGGGTTGGACAAAACAGTCTCATGTCTACTCCTGCTGTATCTGCTGTCATCCGTGAAAGAATTGGTGCAGATgtaagtttgattcttaatgaaggacagtctttagcagtatgaatatttacttgttattcctttatactgtctaatgaataacctgac-tgttggtttataaacacatgaacaaaag----
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA05G34790.1 (Glycine max), 5'ss of exon 4
GGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatat-cttcctctaaactcatactacttacttttctcttgggttgttat-ctaaggctatgcat-gtttgc---aacatg--taatgacgtg-atgagaaactaacccgagatccaatttcag---------------------------------------------------
| ||||||| ||||| || |||||||| ||| |||||||||| | |||| ||||||||||||||||| ||| |||| ||||||||||| || ||||||||||| || || || | | | || ||| | | | || |||| || || | | | |||| | || ||| |||| | || | | | | | ||||
GTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTGCTTTCAACTCCTGCAGTATCTGCTGTTATACGTGAAAGAGTTGGAGCTGATgtgagtaatgttttctacagtttgcttctcgttatctgtacttctctttattatgcttagaatgcgttttgtttcctcaaagatgatccatgattttcatagtggaattgcatatggtaacatttttttctcctgagttaaagcaaaatagtggataaaaaattgtattatctgtacag
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: GLYMA08G04890.1 (Glycine max), 5'ss of exon 4
GGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatat-cttcctctaaactcatactacttacttttctcttgggttgttat-ctaaggctatgcat-gtttgc---aacatg--taatgacgtg-atgagaaactaacccgagatccaatttcag---------------------------------------------------
| ||||||| ||||| || |||||||| ||| |||||||||| | | || || |||||||||||||| ||| |||| ||||||| | | || ||||||||||| || || || | | | || || || | || |||| || || | || | |||| | || ||| |||| | || | | | | | ||||
GTCAGCAGCAAATGGAGTAAGACGTGTTTGGATTGGTCAAAATGGATTACTTTCCACTCCTGCAGTATCTGCTGTTATACGTGAAAAACTTGGAGCTGATgtgagtaatgttttctacagtttgcttctcgttgtttgaacttctctttattatgcttagaatgtgttttgtttcctcaaagatgatccatgattttcatagtggaattgcatatggtaacatttttttctcctgaattaaagattaatagtggataaaaaattgtattatctgtacag
upper sequence: AT1G70730.1 (Arabidopsis thaliana), 5'ss of exon 4
lower sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 5
GGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatatcttcctctaaactcatactacttacttt-tctcttgggttgttatc-taaggctatgcatgtttgcaacat-gtaatgacgtgatgagaaactaacccgagatccaatttcag--------------------------------------------
|||||| || ||||| || ||| ||| |||||||||||||| | |||| ||||||||||| ||||||||| | || ||||||||||| ||| ||||| || || | || || ||| |||||| | | || | | | | | | | || || | | | | | || | || | || ||
GGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGTCAAAATGGGTTGCTTTCAACTCCTGCTGTATCAGCTGTCATCCGTGAAAGAGTGGGGAAAGATgtaagtaatttggcttcaactatctacatcttactgtatgtccttcttcgccgccgcacgtccccccacccccccagtttcatttttaaatattgtttgcttgcagttaggaataggttgagaacaacaaaaataatgaatttgtatatgtactatattaaatcagMapped 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|19878337|gb|AU239168.1|AU239168EST: TATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGAT GGATCTAAAGCCACAGGAGCATTTATCTTAACAGCAAGTCATAATCCTGGT
genomic: TATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatatc ... ccaatttcagGGATCTAAAGCCACAGGAGCATTTATCTTAACAGCAAGTCATAATCCTGGT
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
GGCAGCAGCTAATGGTGTTAGACGTGTGTGGGTTGGTCAAAACAGTCTGCTATCAACTCCTGCAGTATCAGCTATTATTCGTGAAAGAGTAGGGGCTGATgtgagatatcttcctctaaactcatactacttacttttctcttgggttgttatctaaggctatgcatgtttgcaacatgtaatgacgtgatgagaaactaacccgagatccaatttcag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT