Sequence
atgc intronic sequence ATGC exonic sequencegtgagtcctataaagtttcagctgaaattgttttcgcttaggctcttgtttgattatgaattcactgtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57410.2 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: LOC_Os08g14460.1 (Oryza sativa), 3'ss of exon 4
gtgagtcctataaagtttcagctgaaattgttttcgcttaggctcttgtttgattatgaattcactgtgttgac-agGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
|| || || | | | |||| ||| | ||||| ||| ||| | || || |||| ||||||||||||||| |||||||| |||||||||| ||| | || ||||| | ||||| ||||||| ||||| ||||| || |||
gttcgttcttcta---tcaattcttgtttgtattctttgccaatcttgaacttctatttatttcttctgaccaccagGAGGCCAAAAACACTGCAACTTTGAAGGCTCAGATTGACAAGCTGCAACAGGAACGCGATGAGTTCCAAAAAATGGTTATTGGCAATCAG
upper sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GRMZM2G147500_T04 (Zea mays), 3'ss of exon 5
gtgagtcctataaagtttcagctgaaattgttttcgcttaggctcttgtttgattatgaattcactgtg-ttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
|| ||||| || ||| || ||| |||| || | || || |||| | ||||| | || ||||| |||||||||||||| ||| |||||||||||||||| ||| | || || || | |||||||| || | ||||| || || || |||
gtttgtcctt----gtatcaactct--ttggtttc--ttcaccattttttggattctaaattcttttcaattaccagGAGGCCAAAAACACTGCTGCTCTGAAGTCTCAGATTGATAAGCTGCAACAAGAACGTGATGAATTTCAGAAAATGGTTATAGGAAATCAG
upper sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA17G07040.2 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------------------gtgagtcctataaagtttcagctgaaattgttttcgct-taggctcttgtttgatta----tgaattcactgtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
| || | || || | | | | ||| | | |||||| | | ||||||| | || ||||||| ||||||||||||||| ||||| | || ||||| ||| | || |||||||||||||||||||| || ||||| |||||||| |||
gtaaggagatgcttggaaatctggttttggcaaacgtaaagcatgctattgtcttgcttagatgaaaagatcagaagtgtgtccattatgcaagatgcaacaatttccttttttacgcagtgatgctgctagattttgtttaactggggttgaattcctgttatt--tagGAAGCTAAAAACACTGCAGCTCTGAAGGCCCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTCCAGAGAATGGTTATTGGTAATCAG
upper sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: GLYMA13G00980.1 (Glycine max), 3'ss of exon 5
-----------------------------------------------------------------------------------gtgagtcc---tataaagtttcagctgaaattgtttt--cgct--taggctcttgtttgatt----atgaattcactgtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
|| |||| | ||| | || | || | ||| ||| | |||||| ||| |||||| | | | | |||| || ||||||||||||||| ||||| |||| ||||| ||| | || ||||||||||||||||| || || ||||| |||||||| |||
gtaaggagtgcttgtatttctggttttggcaaacctaaagcatgttattgtcttgcttagatgaaaagattagaagtgtgtctgttagtcaagatgtaacgatttccttatttatgcagtgatgctactagatttttgtttaatttgggtagaattccttttat--atagGAGGCTAAAAACACTGCAGCTCTGAAGGCTCAAATTGAGAAGCTGCAACAGGAGAGGGATGAATTTCAGAGAATGGTTATTGGTAATCAG
upper sequence: AT5G57410.3 (Arabidopsis thaliana), 3'ss of exon 5
lower sequence: Vv11s0052g00890.t01 (Vitis vinifera), 3'ss of exon 5
-------------------------------------gtgagtcctataaagtttcagctgaaatt--gttttcgcttaggctcttgtttgatta-tgaattcactgtgt-tgac-agGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
|| | | || ||| | | | | | || || ||||| || | | ||||| ||| ||||||| ||| || |||||||| ||| |||| || ||||| || ||||||||| |||||||||| ||||||||||| |||||||| |||
gttaggaacacttaaattttgtaaagtgaaataatctaggaaattggaattaccctattagacattctatgtcagttgtgtctgtttgttgatcggtgtagtagttgtgtatgattagGAAGCAAAAGCTACAGCAGCTTTTAAGGCTCAAATAGAAAAATTGCAGCAGGAGCGGGATGAATTTCAAAGGATGGTTATTGGTAATCAGMapped 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|86047423|gb|DR343178.1|DR343178EST: TGCAACAATTACCAGAACC GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAG
genomic: TGCAACAATTACCAGAACCgtgagtccta ... gtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAG
EST:
gi|86047424|gb|DR343179.1|DR343179EST: TGCAACAATTACCAGAACC GAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAG
genomic: TGCAACAATTACCAGAACCgtgagtccta ... gtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctgaaattgttttcgcttaggctcttgtttgattatgaattcactgtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
gtttgat putative branch site (score: 5)
tttgattatgaatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtgagtcctataaagtttcagctgaaattgttttcgcttaggctcttgtttgattatgaattcactgtgttgacagGAAGCCAAAAACACTGCAGCTTTGAAGTCTCAGATTGAAAAGTTACAGCAGGAGAGGGATGAATTCCAAAGGATGGTGATTGGTAACCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG