Sequence
atgc intronic sequence ATGC exonic sequenceCCTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAGgtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcag
Basic information
species | Arabidopsis thaliana |
transcript | AT1G57870.1 |
intron # | 10 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G57870.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GRMZM2G138676_T02 (Zea mays), 5'ss of exon 9
CCTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAGgtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcag
||||||||||||| |||||||||||||| ||||| ||||| ||||| ||||| | || || | | || | | | | | ||| || | ||||| | | || | | | | |||| || |
GCTCTGTTTCCTGGAGAAAGTGGAGTCGACCAACTAGTTGAGATCATCAAGgtgattttcttac----ggtatccatatgacca--tatctctactgttttgctgccttcttttgcaccatgacatattgaggcatagcatctgcatcttgcag-------------------------------------------------------------------------------
upper sequence: AT1G57870.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA12G28730.2 (Glycine max), 5'ss of exon 9
CCTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAGgtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcag
|| |||||||||| || |||||||| ||||| || ||||||||||| |||||| ||| | ||| ||| |||| | | || |||| | || | || || || || | | | | | ||| | | ||
CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt-accatccatttttttcaattaatctggattt-----ggctatcctagattatgaaatgtttcttttagacattatatgtacaatgaattcagttg----------------------------------------------------------------------------
upper sequence: AT1G57870.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: GLYMA16G00400.1 (Glycine max), 5'ss of exon 8
CCTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAGgtagtatttttgctatcaattcttttagggttagttgtatttacaa----agaaaatgacatctttagagctggcactg-actaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcag
|| |||||||||| || |||||||| ||||| || ||||||||||| |||||| ||| | ||| || |||| | | || |||||| | ||| |||| || || | || | | ||| | | | ||
CCCTTGTTTCCTGGAGAGAGTGGAGTTGATCAGCTAGTTGAAATCATCAAGgtaaggattt-accatccatgtttttcaattaatctggatttactatcttagatgatgaaatattctttttagacatcatatgtacagtaaatt-cggttgg-------------------------------------------------------------------------------------
upper sequence: AT1G57870.1 (Arabidopsis thaliana), 5'ss of exon 10
lower sequence: PP1S74_168V6.1 (Physcomitrella patens), 5'ss of exon 7
CCTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAGgtagtatttttgctatcaattcttttagggt-tagttgtattta-caaa-gaaaatgacatctttagagctggcactgactaata-gtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcag---------
||| |||| ||||| |||||||||||||||||| | || |||||||| ||||||| | | | || | || || || | | || | | || || | | | | | | | | ||| | ||| | | | || | || || || | || | | | | | | || | | || |
CCTTTGTTCCCTGGAGAAAGTGGAGTCGATCAATTGGTGGAAATCATCAAGgtagcttacatatggtagatgttgaggaagtgcaggggtctacagcagatgtcggtgctggtgtttgggttttgtccgtttgaaatgttgtgttgcgttgaaaggttgtagctggtacttgctcggtgtgatgttagttatgacttcgctagaatggatatgtaggacttatgggtagttgggtgttaatgttagMapped 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|116422944|gb|EG465536.1|EG465536EST: CTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAG GTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTAC
genomic: CTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAGgtagtatttt ... tgtcatgcagGTTTTGGGTACACCAACAAGGGAGGAGATCAAATGCATGAATCCAAACTAC
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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
CCTCTGTTTCCTGGCGAAAGTGGAGTCGATCAACTTGTTGAAATCATAAAGgtagtatttttgctatcaattcttttagggttagttgtatttacaaagaaaatgacatctttagagctggcactgactaatagtttctcactgctgattatattttttttataaaactttaccaccatttttgtagtaggactcgtacattctctcttcatggttttttaattgtcatgcag
- - - - - - - - - AGTGGA
- - - - - - - - - GTGGAG