Sequence
atgc intronic sequence ATGC exonic sequencegtaggtttagtaagaataccaattcaatgtctcgaaaagaatcattttggattccttgtttgacacagctcttatgataatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
Basic information
species | Arabidopsis thaliana |
transcript | AT4G37640.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os03g10640.1 (Oryza sativa), 3'ss of exon 5
---------gtaggtttagtaagaataccaattc---aatgtctcgaaaagaatcattttggattccttgtttgacacagctcttatgat-aatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
|| || | | | || || ||| || | |||| | || | | | | ||| || | |||||| ||||||||| | |||||||| ||| || | ||||| |||||||||||||||||||| ||||| || || || || || || || |||||||| || ||
taaactaacataaaatttattaatgtggaaaatcaagaatttcctagtttgtttcataacttactcttgactgttctttgtacttctgcttggcattcagGGAGTGCTCCTCTTACTGCTGTCCAACTGCTCTGGGTTAACATGATCATGGACACACTAGGAGCACTGGCATTGGCAACTGAACCTCCAAACGATGAACT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G118919_T01 (Zea mays), 3'ss of exon 3
-------------------------------gtaggtttagtaagaataccaattcaatgtctcgaaaagaatcatt--ttggattccttgt-----ttgacacagctcttatgataat-cttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
| || | || ||| | | | || | |||| |||| || | | | | | || || | ||||| || || || | ||||| || || || | ||||||||||||||||||||||| || |||||||| || || || || ||||| || |||||||||||
gtaaaaaaaaaaacctcacgctgctgcgttcatctgtaggtgactgattccagtctgaatctgaaataatagacattgactggagcccgtaaacaaactcataaaatgtgcttgtcgattcatcagGGAGCGCGCCCCTGACTGCGGTGCAGCTGCTCTGGGTGAACATGATCATGGACACGCTGGGAGCTCTGGCGTTGGCCACGGAGCCCCCCAACGACGAGCT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G006977_T01 (Zea mays), 3'ss of exon 5
----------------------------gtaggtttagtaagaat--accaattcaatgtctcgaaaagaatcattttggattcct------tgtttgacaca------gctcttatgataatc-----ttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
|| ||||| | || | || | || | || || || | ||||| | | | | || | || || | ||| | || |||||| ||||||||| | |||||||| |||||| | ||||| |||||||||||||| ||||| || || || || || || ||||| || |||||| | || ||
gtacatccgatatcctgtatatgagttcgt-ggtttggaaatcctctactacttgagcgtatcctgaatgtactttttgtttatttcataaatatatgtctcattgttcgcattcatgctgattgctgattcagGGAGTGCTCCTCTCACTGCTGTGCAATTGCTCTGGGTCAACATGATCATGGATACACTGGGTGCGCTGGCATTGGCGACAGAACCCCCAAACAATGAACT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G317270_T01 (Zea mays), 3'ss of exon 3
gtaggtttagtaagaat--accaattcaatgtctcgaaaagaat-cattttggattccttgtttgacacagctcttatgataatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
||| | || ||||| || |||| | ||| | | || | | | ||| || | | | ||| | | | | |||| || ||||| | || || || || || ||||||||||||||||||||||||| || ||||| || || | || || ||||| || |||||||||||
gtaagcttccaaagaactggtgaaagcaatctgtcgccatgcatgcttgcttgatctgctgct-gctgctgcttgtgttgtgga-tccagGGAGCGCTCCCCTGACAGCCGTGCAGCTGCTGTGGGTGAACATGATCATGGACACGCTGGGAGCGCTGGCGCTGGCCACGGAGCCTCCGAACGACGAGCT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA01G40130.2 (Glycine max), 3'ss of exon 5
----------------------------------------------------------------------------gtaggtttagtaagaataccaattcaatgtctcgaaaagaatca--ttttggattccttgtttgacacagctcttatgata--------atcttc-------agGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
| | ||| | | || | | || | || || |||| || | || | ||||||||| || ||| ||||| ||| || | || ||||||||| | ||||||||||||||||| ||||||||||| ||||| |||||| | ||||| || || ||||| || || |
gttagaaagttaatttaattttgttaccacaaaatagggttatgtacttacataaacagcaaggaactgcactttttttgttttcacaccagcctgcatgacagattataaataaaaacactttttttgttttcttcttattagttatcttatgatcttacatgtattttctctatccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA11G05190.2 (Glycine max), 3'ss of exon 5
----------------------gtaggtttagtaagaataccaattcaatgtctcgaaaagaat-cattttggattccttgtttgacac-agc--tcttatgat---------aa------tcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
|| | | | || | | ||| | | ||||| || | || | || ||||||||| || ||| |||||| ||| || | || ||||||||| | ||||||||||||||||| ||||||||||| ||||| |||||| | ||||| || || ||||| || || |
gttagaaagttaatttaattttgttaccccaaaacaatagcctgcatgacaggttataaaaactgttttttgtgttttcttcttattattagttatcttatgatcttacatgcaatttctctctccagGAACTGCACCCCTCACAGCTGTTCAACTCTTGTGGGTGAACATGATAATGGACACACTGGGAGCACTTGCTCTTGCTACTGAACCTCCAAATGATGATTT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA05G22420.1 (Glycine max), 3'ss of exon 5
-------------------------------------------------gtaggtttagtaagaatac--caattcaatgtctcgaaaagaatcattttggattccttgtttgacacagct-cttatgat-aatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
| | | | | | | | | ||||| | | | || || | | || | | || | | | | | ||||||||| ||||| || | || ||||||||| | ||||||||||||||||| |||||||| || ||||| ||||| | || || || ||||||| || || |
gttaaaacattatgcctaattagtcttacatgcatcctttcattcatttttcattctgttcaaagtgcagtggtaaaatgtgtttatagaaa--atagaaaactttttatctcacgattttgcgtgtatttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACTCTAGGAGCACTTGCACTTGCAACTGAACCACCAACTGATGATTT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G17450.1 (Glycine max), 3'ss of exon 6
-----------------------------------------------------------gtaggtttagtaagaataccaattcaatgtctcgaaaagaatcattttggattccttgtttgacacagctcttatgataatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
| || ||| || | || | ||| || | |||| || ||| ||| | | || | ||||||||| ||||| || | || ||||||||| | ||||||||||||||||| |||||||| || ||||| ||||| | || || || || |||| ||| || |
gttaaaaaattttgcctaattagcttacatgcatcctctcattcatttttcattccgttcaaagtgcagtggtaaaatgtgtttataaga--aaaataaaacttttttatctcacgattttacatgtatttgattttgatcttcagGCAGTGCACCCCTCACAGCTGTTCAACTTTTGTGGGTGAACATGATAATGGACACGCTGGGAGCACTTGCACTTGCAACTGAACCTCCAACCGATGATTT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0129g00110.t01 (Vitis vinifera), 3'ss of exon 4
------------------gtaggtttagtaagaataccaattcaatgtctcg--aaaagaatcattttggattcct---------tgtttgacacagctcttatgataatc--ttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
| || | || | ||| ||| | | ||| || || || || | ||| | | | || | || | || ||||| |||||| | || |||||||| | ||||||| |||||||||||||| ||||| ||||||||||| ||||| || |||||||| | || || |
gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgtcaaataaacttcttcttttttctccctacattttttttattccttttttttttcaaacacttaagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACCGAGCCACCTACTGATGACTT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv07s0129g00180.t01 (Vitis vinifera), 3'ss of exon 5
------------------gtaggtttagtaagaataccaattcaatgtctcg--aaaagaatcattttggattcct---------tgtttgacacagctcttatgataatc--ttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
| || | || | ||| ||| | | ||| || || || || | ||| | | | || | || | |||||||| |||||| | || |||||||| | ||||||| |||||||||||||| ||||| ||||||||||| ||||| || |||||||| | || || |
gtaagaagaccccatcttgcttcttccatttcaaagttacttccttgttttgtcaaataaacttcttcttttttctccctacattttttttattccttttttttttcaaacacttcagGAAATGCTCCCCTCACGGCTGTTCAGCTTCTGTGGGTCAACATGATCATGGATACACTGGGAGCTCTTGCATTAGCAACTGAGCCACCTACTGATGACTT
upper sequence: AT4G37640.1 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: PP1S37_351V6.1 (Physcomitrella patens), 3'ss of exon 7
------------------------------------------gtaggtttagtaagaataccaattcaatgtctcga--aaagaatcattttggattccttgtttgac---aca-gctcttatgataatct---tcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
| || | | | |||||||| | || | || ||| || || | ||| ||| || || || | | |||| | ||| ||| | || || ||||| | |||||||| ||| |||| |||||||| || || || |||||||| ||||| ||||| || |||||||||||
gtaaattttcagtattgcgcttctcggtttttttgaattaaaggagacagaccatgtataccaatgaaccacctagtttaagagatcccagtgatttttcattgtgatcttacatacttgtacgacgttttgtcccagGTACTGCGCCTCTTACCGCAGTTCAGCTCTTGTGGGTAAACCTGATTATGGACACCCTAGGGGCACTTGCTTTGGCTACTGAGCCTCCTAACGACGAGCTMapped 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|116395208|gb|EG437800.1|EG437800EST: GTTAATGTTGGTGCACTGGTTGTTA-CTTCTCTTCAGCTTGTTTAACCCG GA-GTGCTCCTTTA-CTGCTG
genomic: GTTAATGTTGTTGCACTGGTTGTTAACTTCTCTTCAGCTTGTTTAACC-Ggtaggtttag ... taatcttcagGAAGTGCTCCTTTAACTGCTG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.cgaaaagaatcattttggattccttgtttgacacagctcttatgataatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
gtttgac putative branch site (score: 4)
tcttc putative PPT
ttatgataat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaggtttagtaagaataccaattcaatgtctcgaaaagaatcattttggattccttgtttgacacagctcttatgataatcttcagGAAGTGCTCCTTTAACTGCTGTTCAATTGTTGTGGGTGAACATGATCATGGACACACTTGGAGCTCTTGCTTTAGCTACAGAGCCACCAAACGACGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT