Sequence
atgc intronic sequence ATGC exonic sequence...gcagtctctaaattgatagtttacttatatagtgattactcttttgggattctatctggcgtccttcatctggatattgaacttgcttcaaactttgtagATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G13430.1 |
intron # | 7 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA17G37540.1 (Glycine max), 3'ss of exon 7
-----------------------gcagtctctaa-attgatagtttacttatatagtgattactcttttgggattctatctggcgtccttcatctggatattgaa--cttgcttcaa----------actttgtagATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
|| ||| |||| || || |||| || || | | | | | | | || | | ||| | ||| | | || || || ||||||||||||||||| |||| ||||||||||| || || |||||||||| ||||||||| | |||||| | |
agtaagtgccttgattctgtacttttgtttctgttggacatagcatagccatcaggtgactatgattgtttgctcat-tttcatgcagcaaatataaaaattacatccttacatgaatggatggtttaccttacaGATTATTGGTGAAATAACTGTGGCTGGTGCAACATATAAATCGATGGAGTTTGTCGGTACAACTGTTGAAAGTTTAAC-
upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: GLYMA20G34160.1 (Glycine max), 3'ss of exon 8
--------------------------------gcagtctctaaattgatagtttac-ttatatagtgattactcttttgggattctatctggcgtccttcatctg-gatattgaacttgcttcaaactttgt--agATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
| || || | | |||| | || | | | || | || | || | | | | | ||| || || | | | |||| ||||||||||||||||| |||||||||| || || ||||||||||| ||| ||||| || |||||| | |||
gtgggtaatgggttcctctcatgtttttccatttgaatgaaatgctgttaatcaaagttatgtgac-atgagtatattataacactgttgtctgttttcttttcgtggtgttgccatttgaaaaaccatcattcagATCATTGGTGAAATATCTGTGTCTGGTGCAACATATAAAACGATGGAGTTTGTTGGGACAACAATTGAAAGTTTAAGT
upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: Vv05s0049g01980.t01 (Vitis vinifera), 3'ss of exon 7
---------------------------------------------------------------------------------gca-gtctctaaattgatagtttacttatatagtgatt-actcttttgggat--tctatctggcgtccttcatctggatattgaacttgcttcaaactttgtagATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
| | | | || | | |||||||| | || || | | |||| || || || | | || | || | || | |||||| ||||||||||||||||||||||| |||| || || || || | ||||| || ||| || ||| | |||||| | | |
gtaagtcttactagcactagtggcgttctttcatttttaaagggcataatctttccacccatggaatatgttgtgtttttaatatgagcccatatcggttgtttacttcgctgatgttttaatggattggtatggccttcctttttttatggtcttgcttcacaaaatggcctttcactttgcagATTATTGGTGAAATATCTGTTTCTGGCGCGACATATAAATCTATGGAATTTGTTGGCACTACTGTTGAAAGTTTAACT
upper sequence: AT4G13430.1 (Arabidopsis thaliana), 3'ss of exon 7
lower sequence: PP1S227_66V6.1 (Physcomitrella patens), 3'ss of exon 7
--------gcagtctctaaat--tgatagtttacttatatagtgattactcttttg-ggattctatctggcgtccttcatctggatattgaacttgcttcaaac--------tttgtagATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
| | | | | || || | ||| | || | ||| | | | | ||| | || || | || || | || || | | | || ||||||| ||||||||||||||||| || |||||||||| |||||||||| || || | | || | |||
gtatggttgtattttatggatcgtgttggttcattt-tgtagaatcgaatttgaagtggagcttcgttgtagtgatcaatgaaaatttctcttttaattaagtcagtctgtttgtgcagATTATCGGTGAAATATCTGTTGCAGGGGCAACTTACAGAGCGATGGAGTTTGTCGGCACTGCCGTTGATGCTATGACG atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gggattctatctggcgtccttcatctggatattgaacttgcttcaaactttgtagATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
atattgaa 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcagtctctaaattgatagtttacttatatagtgattactcttttgggattctatctggcgtccttcatctggatattgaacttgcttcaaactttgtagATTATTGGTGAAATATCTGTTGCTGGTGCAACTTACAAGACGATGGAGTTCAGTGGTACAACTATCGAAAGTCTGAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - -ctctaaa
- - - - - - - - - - - - - - - - - - - - - - - - - -ctatctg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttgcttc