Sequence
atgc intronic sequence ATGC exonic sequencegtacatttaactcggttacaagcagtggacttttggccaagacgtagtcagacaaaactgttgttgttctctcttatcatttctgtggtctcttaataggttccaaatgcctcacagtttttgctctcttgtcgttttgattgccttgtaacagGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
Basic information
species | Arabidopsis thaliana |
transcript | AT4G34900.1 |
intron # | 10 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GRMZM2G050984_T01 (Zea mays), 3'ss of exon 6
gtacatttaactcggttacaagcagtggacttttggccaagacgtagtcagacaaaactgttgttgttctctcttatcatttctgtggtctcttaataggttccaaatgcctcacagtttttgctctcttgtcgttttgattgccttgtaacagGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
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-----gtgaggtccgacacatggatgtaccccttctgcatgattt--ttacacta-------gttgtactttttt-tcattacttttatttataagttg--tgccaatacaatgaggtgatgggattccatctgttt---------------agGTTCCTAATGCATCACCAACAGCAGCCTCTGCTAGTTCAGATCTGTATGGAGCTGCAGTTTTGGATGCTTGTCAACAAATCAAGGTTCGAATGGAACCCA
upper sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA13G41520.1 (Glycine max), 3'ss of exon 11
gtacatttaactcggttacaagcagtggacttttggccaagacgtagtcagacaaaactgttgttgttctctcttatcatttctgtggtctcttaataggttccaaatgcctcacagtttttgctctcttgtcgttttgattgccttgtaacagGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
| | | | | ||| | | | | | | | | ||| | || || | | ||| || | | || | | || | | ||||||||||||| || || || || |||||||| ||||||||||||||||| || || ||||| || || |||||||| || || | | | ||||| |||
----------------------------------------------------tatcattttctattttccccccatttacctttcttgaatctggggatattgtttctgatactaaatttctgtgttgtcctcatgcttgctggcaaat--tagGTTCCTAATGCTTCTCCAACAGCAGCTTCTGCAAGTTCTGATATGTATGGAGCAGCGGTTTTGGATGCATGTGAGCAAATAATGGAACGCATGGAACCTA
upper sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: GLYMA15G03870.1 (Glycine max), 3'ss of exon 10
gtacatttaactcggttacaagcagtggacttttggccaagacgtagtcagacaaaactgttgttgttctctcttatcatttctgtggtctcttaataggttccaaatgcctcacagttt---ttgctctcttgtcgttttgattgccttgtaac-agGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
| | || | | || | ||| | ||| | || | | || | | | | ||||| | | || | || |||| || ||||||||||||| ||| | || || |||||||| ||||||||||||||||| || || ||||| || || |||||||| || || ||| | ||||| |||
----------------------------------------------------------tccttttctattttcctcccatgtaccctttcttgaatatggggactattgttttttattctaaattgctgtgatatcctcatggttgctgcaaaattagGTTCCTAATGCTTCAGCAACAGCAGCTTCTGCAAGTTCTGATATGTATGGAGCAGCGGTTTTGGATGCATGTGAGCAAATAATGGCACGCATGGAACCTA
upper sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: Vv06s0004g02030.t01 (Vitis vinifera), 3'ss of exon 10
gtacatttaactcggttacaagcagtggacttttggccaagacgtagtcagacaaaactgttgttgttctctcttatcatttctgtggtctcttaataggttccaaatgcct-cacagttttt---gctctcttgtcgttttgattgccttgtaacagGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
| | || | | | | |||| || ||||| | ||||| | | | |||| ||| | || | | ||||| || || | | | |||||||||||| | |||| || || |||||||| ||||||||||||||||| |||||||||||||| ||||| ||||| || | |||| | ||||||||
-------------------------------------------------------gattattcat-tattttactatc-cttttgtggattattaat-gaacctagttgccgacactgattctcgtatttacttgtacttgtgttgctgctaaatcagGTTCCTAATTCAACACCAACAGCAGCTTCTGCAAGTTCTGATATGTATGGAGCTGCAGTTTTAGATGCTTGCGAGCAAATAAAAGCACGGATGGAGCCGA
upper sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ27160 (Selaginella moellendorffii), 3'ss of exon 10
gtacatttaactcggttacaagcagtggacttttggccaagacgtagtcagacaaaactgttgttgttctctcttatcatttctgtggtctcttaataggttccaaatgcctcacagtttttgctctcttgtcgttttgattgccttgtaac--agGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
|| | ||| | || ||| ||| || | |||| || |||| || ||||| || |||||||| ||||||||||| ||||||||||||||||| || ||| | || || || | || || | || ||| ||| ||
---------------------------------------------------------------------------------------------------gtac--gctgcttttcacctttcaagttctgctcaccac----gtcttggaatgtagGTACCAAATGCTTCGCCTACTGCGGCTTCTGCGAGCTCTGATATGTATGGTGCCGCTGTTATCGATGCATGCAACCAAATCAAAGAAAGGATGAGACCAT
upper sequence: AT4G34900.1 (Arabidopsis thaliana), 3'ss of exon 10
lower sequence: EFJ33495 (Selaginella moellendorffii), 3'ss of exon 10
gtacatttaactcggttacaagcagtggacttttggccaagacgtagtcagacaaaactgttgttgttctctcttatcatttctgtggtctcttaataggttccaaat-gcctcacagtttttgctctcttgtcgttttgattgccttgtaacagGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
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-----------------------------------------------------------------------------------------------gtacgctgcttttcacctttcaagttctgctcacca--cgtcttggaa----tgta--agGTACCAAATGCTTCGCCTACTGCGGCTTCTGCGAGCTCTGATATGTATGGTGCCGCTGTTATCGATGCATGCAACCAAATCAAAGAAAGGATGAGACCAT atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gttccaaatgcctcacagtttttgctctcttgtcgttttgattgccttgtaacagGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
ttgcctt CT-rich tract
ttttgatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacatttaactcggttacaagcagtggacttttggccaagacgtagtcagacaaaactgttgttgttctctcttatcatttctgtggtctcttaataggttccaaatgcctcacagtttttgctctcttgtcgttttgattgccttgtaacagGTTCCTAATGCGTCACCTACTGCTGCTTCTGCGAGTTCTGATATGTATGGTGCTGCAGTTTTAGACGCTTGTGAGCAGATTATAGCAAGAATGGAGCCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA