Sequence
atgc intronic sequence ATGC exonic sequencegtaatagagtcaattaacacaatcgattaatcttaaaccaagtgggaagaagaagctgaaaagagagagactaatcttcttcttcttcttcctctctgtatttttctcattctcttcgatttgtttgcttgctagTGACTAGTGAGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCACACACATCGACCGCAGATCTACTTACTTGGTCGGAAGTTCCACCGCCGGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G78150.2 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G78150.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G10930.1 (Glycine max), 3'ss of exon 1
gtaatagagtcaattaacacaatcgatta-atcttaaaccaagtgggaagaagaagctgaaaagagagagactaatcttcttcttcttcttcctctctgtatttttctcattctcttcgatttgtttgcttgctagTGACTAGTGAGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCACACACATCGACCGCAGATCTACTTACTTGGTCGGAAGTTCCACCGCCGGA-
| ||| | | || ||| || || | | | | || || ||| | | | | || | || || || || | || || | ||| || |||||||||||| ||||||||||| ||||||||||| || || |||||||| ||||| ||| | ||| ||| | |
---gcacggtcccccccccccctccattttatttttcttgtcattttttgtatatttattgaaagaagggacgagcccaaagtgaagaatgagtaataagggttaattggtt------gagcagtgagcagGGTATTG-----TAGCTGAACGA-TATGGAGAGAAGCACTCCGGTGAGGAAGCCACACACTTCAACTGCAGATCTGCTTACGTGGCCTGAAACACCAATTTCTCAT
upper sequence: AT1G78150.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA06G10930.3 (Glycine max), 3'ss of exon 1
gtaatagagtcaattaacacaatcgatta-atcttaaaccaagtgggaagaagaagctgaaaagagagagactaatcttcttcttcttcttcctctctgtatttttctcattctcttcgatttgtttgcttgctagTGACTAGTGAGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCACACACATCGACCGCAGATCTACTTACTTGGTCGGAAGTTCCACCGCCGGA
| ||| | | || ||| || || | | | | || || ||| | | | | || | || || || || | || || | ||| || |||||||||||| ||||||||||| ||||||||||| || || |||||||| ||||| ||| | ||| |||
---gcacggtcccccccccccctccattttatttttcttgtcattttttgtatatttattgaaagaagggacgagcccaaagtgaagaatgagtaataagggttaattggtt------gagcagTGAGCAGGGTATTG-----TAGCTGAACGA-TATGGAGAGAAGCACTCCGGTGAGGAAGCCACACACTTCAACTGCAGATCTGCTTACGTGGCCTGAAACACCAAT------
upper sequence: AT1G78150.2 (Arabidopsis thaliana), 3'ss of exon 1
lower sequence: GLYMA04G11160.4 (Glycine max), 3'ss of exon 1
gtaatagagtcaattaacacaatcgattaatcttaaaccaagtgggaagaagaagctgaaaagagagagactaatcttcttcttcttcttcctctctgtatttttctcattctcttcgatttgttt-gcttgctagTGACTAGTG-AGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCACACACATCGACCGCAGATCTACTTACTTGGTCGGAAGTTCCACCGCCGGA
| ||| | | || | || | | | || || || || ||| | | || || | ||| ||| || | || || | ||| || || ||||||||||| | ||||||||| ||||||||||| || || |||||||| ||||| ||| | ||| |||
---gcacggtccccccccctttccatttttttttttgtttttaattgaaagagggacgaggcgaaagtgaagaatgaagaggaatg-----------agaaatagctaataagtgttaattggttgagcagGGTATTGTGTTGTGTAGCTGAAGGACATGGAGAGAAGCAATCCGGTGAGGAAGCCACACACTTCAACTGCAGATCTGCTTACGTGGCCTGAAACTCCCAT------Mapped 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|47831749|gb|CK121433.1|CK121433EST: GTAGAGAAGAAGCTTCCAGATCAAAATGAGATTTACGAACAAAGTAAAGG TGACTAGTGAGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCAC
genomic: GTAGAGAAGAAGCTTCCAGATCAAAATGAGATTTACGAACAAAGTAAAGGgtaatagagt ... tgcttgctagTGACTAGTGAGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCAC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tcttcttcttcctctctgtatttttctcattctcttcgatttgtttgcttgctagTGACTAGTGAGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCACACACATCGACCGCAGATCTACTTACTTGGTCGGAAGTTCCACCGCCGGA
tttgttt CT-rich tract
tgtattttt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaatagagtcaattaacacaatcgattaatcttaaaccaagtgggaagaagaagctgaaaagagagagactaatcttcttcttcttcttcctctctgtatttttctcattctcttcgatttgtttgcttgctagTGACTAGTGAGTGAGAGAGTATGGAGAGAAGTACTCCGGTGAGAAAGCCACACACATCGACCGCAGATCTACTTACTTGGTCGGAAGTTCCACCGCCGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT