Sequence
atgc intronic sequence ATGC exonic sequencegtaaagttctaattcccactataaaaggagcaaatttgtgatttcaaatatcagtcatcgtctgatagtttgttgacattatgcagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACAAAAACCATGTCAGGCCTCTGCAAGAGCAACTTGAGAACCCACCAAAACC
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34570.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA12G04480.1 (Glycine max), 3'ss of exon 9
--------------------------------------------------------------------------------------------------------------gtaaagttctaattcccactataaaaggagcaaatttgtgatttcaaat--atcagtcatcgtctgatagtttgttgacattatgcagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACAAAAACCATGTCAGGCCTCTGCAAGAGCAACTTGAGAACCCACCAAAACC
| || | | || || || | | | ||| | | |||| || | | ||| |||| | |||| |||||||| ||||||||||||||||| ||||| ||||| ||||||||| || ||||| || || |||| || || || |||||| |||||||||
gtatgcaaattatgccagctttgctagacttaaatttgtactcagacgcacataccatcttaaatccgactttcatgggttcaatagagatttctcattgtttgattgtagggaaatacagcttttatataaaaggaaaattgacattagatattggactgatcaatccatctgtcatatcctgtttttgt----cagACCTTGTTCCAGGTGATTTTATCCATGTTATTGGGGATGCACATGTTTACCGCAATCATGTGAGACCCTTGCAGGAACAGCTCCAGAACCAACCAAAACC
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA04G01240.1 (Glycine max), 3'ss of exon 9
--------gtaaagttcta-attcccactataaaaggagcaaattt----gtgatttcaaatatcagtcatcg--tctgatagtttgttgacattatgcagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACAAAAACCATGTCAGGCCTCTGCAAGAGCAACTTGAGAACCCACCAAAACC
| | || | | | ||||| | || || || || |||| || | | ||| | ||| | |||| || | ||||||| |||| ||||||||||||||||| ||||| ||||| ||||||||| || ||||| |||||| |||| ||||| || | |||| ||||||||
agaagcttattgattttgataatatcactagagaaaatacagcattaaaagtaatttaaacacaaaataatcaatctttatactgtgtttttcttgt-cagATCTCATTCCAGGTGATTTTATCCATGTTATTGGGGATGCACATGTTTACTGCAATCATGTGAGGCCTTTGCAGGAGCAGCTCCATAACCAGCCAAAACC
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA06G01280.1 (Glycine max), 3'ss of exon 9
-gtaa-agttctaat--tcccactataaaaggagcaaattt----gtgatttcaa---atatcagtcatcg--tctgatagtttgttgacattatg-cagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACAAAAACCATGTCAGGCCTCTGCAAGAGCAACTTGAGAACCCACCAAAACC
|| ||| | || | ||||| | || || || || |||| || | | | ||||| | ||| | ||| | || ||||||| |||||||||||||||| ||||| ||||| ||||||||| ||||| || || || |||||| |||| ||||| || | |||| ||||| ||
cttattggttttgataatatcactagagaaaatacagcattaaaagtaatttaaacgtaaaataatcatcaatctttatactatgtctctttcttgtcagATCTCATTCCTGGTGATTTTATTCATGTTATTGGGGATGCTCATATTTACCGCAATCACGTGAGGCCTTTGCAGGAGCAGCTCCATAACCAGCCAAAGCC
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA11G12280.1 (Glycine max), 3'ss of exon 8
---------------gtaaagttctaattcccactataaaaggagca--aatttgtgatttcaaatatcagtcatcgtctgatagtttgttgacattatgcagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACAAAAACCATGTCAGGCCTCTGCAAGAGCAACTTGAGAACCCACCAAAACC
| | | | | | |||||||||| | | | ||| || | | | |||| | | || || | |||| |||||||| ||||||||||||||||| || || ||||| ||||||||| || ||||| || || |||| || || || |||||| |||||||||
tgatagtcttaccgtagagaaatacagctttta-tataaaaggaaaattgacattagatatcggac-tgatccatccatctgccatatcctgttcttgt-cagACCTTGTTCCGGGTGATTTTATCCATGTTATCGGGGATGCACATGTTTACCGCAATCATGTGAGACCCTTGCAGGAACAGCTCCAGAACCAACCAAAACC
upper sequence: AT4G34570.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv03s0038g04500.t01 (Vitis vinifera), 3'ss of exon 10
------------gtaaagttctaattcccactataaaaggagcaaatttgtgatttcaaatatcagtcat-cgtctgatagtttgttg-acattatgcagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACAAAAACCATGTCAGGCCTCTGCAAGAGCAACTTGAGAACCCACCAAAACC
|| ||| | ||| | ||| ||||| ||| | | |||| | | | || | || | |||| ||||||||||||||||| |||||||| ||||| || |||||||||| | ||| ||||||||||||| ||||| ||| |||| | || |||||
ttatcttcttcttcttcttttctatttttaatattcagctcattggtttttgattatttgtattaaagaaatgtctttaattgtattttatcttgtacagACCTTGTTCCTGGTGATTTCATCCATGTTATTGGGGACTCTCATGTTTATCTGACTCATATCAGGCCTCTGCAGGAGCAGCTTCAGAAGCTTCCTAAACCMapped 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|19741045|gb|AU226398.1|AU226398EST: TAACATTGCCTCATACTCCCTTCTTACATGCATTCTTGCTCACGTCTGCG ATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACA
genomic: TAACATTGCCTCATACTCCCTTCTTACATGCATTCTTGCTCACGTCTGCGgtaaagttct ... cattatgcagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACA
EST:
gi|124880789|gb|EH959691.1|EH959691EST: TAACATTGCCTCATACTCCCTTCTTACATGCATTCTTGCTCACGTCTGCG ATCTTGTTCCTGGTGATTTTA
genomic: TAACATTGCCTCATACTCCCTTCTTACATGCATTCTTGCTCACGTCTGCGgtaaagttct ... cattatgcagATCTTGTTCCTGGTGATTTTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aaatttgtgatttcaaatatcagtcatcgtctgatagtttgttgacattatgcagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACAAAAACCATGTCAGGCCTCTGCAAGAGCAACTTGAGAACCCACCAAAACC
tgttgac putative branch site (score: 3)
atttcaaatat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaaagttctaattcccactataaaaggagcaaatttgtgatttcaaatatcagtcatcgtctgatagtttgttgacattatgcagATCTTGTTCCTGGTGATTTTATCCATGTGATTGGAGATGCTCATGTTTACAAAAACCATGTCAGGCCTCTGCAAGAGCAACTTGAGAACCCACCAAAACC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCA