Sequence
atgc intronic sequence ATGC exonic sequencegtatttcctgccacaccctttcaacaatacatacaaaacagtgaaaaaaaatgatttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT1G31440.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G31440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA09G34950.1 (Glycine max), 3'ss of exon 10
---gtatttcctgccacaccctt--tcaacaatacatacaa--aacagtgaaaaaaaatga--tttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
| ||| | || || || | ||| || || | | | ||| | || | || | || || | || ||| | |||| | | || ||||| |||||||||| ||||||||| |||||||||||||| ||||| || ||||||| ||| || | || || |||||||
atgatcttttttttcagacttttaagttataatctttattgccaatatcagactgatttgagctgtatttttattatccttttggttgttacatttctagGTTGGACCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTAGAGAGACAGGACATGATACCAGCCAGCAAGA
upper sequence: AT1G31440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: GLYMA01G35400.1 (Glycine max), 3'ss of exon 9
-----gtatttcctgccacaccctttcaacaatacatacaa--aacagtgaaaaaaaatga--tttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
||||| | | | ||| || | | | | ||| | || | || | || || | || ||| | ||||| | | || ||||| |||||||||| ||||||||| |||||||||||||| ||||| || ||| ||| ||| || | || || |||||||
ttgtgatatttttttcagacattaagttataatctttattgccagtatcagactgatttgagctgtatttgtattatccttttggttgttacatttccagGTTGGCCCCAATGGATGGTCTGAAGGAGAATGCAAAGGCAATGCTGGATGGTTTCCCTCTGCTTATGTACAGAGACAGGACATGATACCAGCCAGCAAGA
upper sequence: AT1G31440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ27680 (Selaginella moellendorffii), 3'ss of exon 8
gtatttcctgccacaccctttcaacaatacatacaaaac-agtgaaaaaaaatgatttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
| || || ||| | ||| | || | | | || |||| ||||| || || ||||||||||||||||||| ||||||||||| ||||||||||| ||| |||| || ||| || | ||| || |||||
------------------------------gtgggtgacgagccaaagtcattgaatgaatgaacgtttttcttttg------------cagGTTTCTACCACTGGCTGGTCAGAAGGAGAATGTAAAGGCAAAGCGGGATGGTTTCCATCTACGTATGTGGAGCGCAGGCAGCGTGTTCCTGCTAGCAAAG
upper sequence: AT1G31440.1 (Arabidopsis thaliana), 3'ss of exon 9
lower sequence: EFJ37265 (Selaginella moellendorffii), 3'ss of exon 8
gtatttcctgccacaccctttcaacaatacatacaaaacagtgaaaaaaaatgatttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
|| ||| | ||| || | | || || ||||| || || ||||||||||||||||||| ||||||||||| ||||||||||| ||| |||| || ||| || | ||| || |||||
---------------------------------gtgggtgacgagccaaagtcattgaatgaatgaacgtttttctttgg--------cagGTTTCTACCACTGGCTGGTCAGAAGGAGAATGTAAAGGCAAAGCGGGATGGTTTCCATCTACGTATGTGGAGCGCAGGCAGCGTGTTCCTGCTAGCAAAG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aacagtgaaaaaaaatgatttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
aaaaaaaatgatttaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatttcctgccacaccctttcaacaatacatacaaaacagtgaaaaaaaatgatttaacaatcttgttctgtttgatgaaacaaattcagGTGGCTGGTACAGGCTGGTCAGAAGGAGAATACAAAGGCAAAGCTGGATGGTTTCCGTCTGCGTACGTAGAGAAACAAGAGAAAGCTCCGGCAAGCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA