Sequence
atgc intronic sequence ATGC exonic sequencegtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: LOC_Os02g50880.1 (Oryza sativa), 3'ss of exon 2
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
| | || | | || || | || ||| | || |||| | | || |||||||| ||| | | | | || | ||| || || | || ||||||||||||||||||| |||||||||||||||||||||||||||||||| ||||| |||||||| |||||||||||||| ||||| |||||||||||||
--------------------gttcattttctccccacaa---ttctcatttagaatagtattatctgtgaggataacatgttgagaaatcataagtcttt---taact-----------tttggg----gttttatggacagATAGATGCAGCTATTAACTCAGGAAATTCAGGTGGCCCAGCTTTTAATGACAGGGGCAAATGTGTTGGTATAGCTTTTCAATCTCTCAAACATGAAGATG
upper sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: GLYMA01G16820.1 (Glycine max), 3'ss of exon 2
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
|| ||| ||| || ||| ||| | | || || || | | ||| | || | | | | || | |||| | | | | || |||||||||| || || ||||| || ||||| ||||| || ||||| ||||||| ||||||||| || || || || || ||||||||||||||||||||||
--------------------gtaacataggttctaagctatcccttttcac-------ttttccatgt---atgccccgcttgtccatttat-atatgttaa---attgaagcgtct--------cttcgaatcctttgcagATAGATGCTGCGATAAATTCTGGGAATTCTGGTGGACCTGCTTTCAATGATAAGGGAAAATGCGTTGGGATTGCATTCCAGTCTCTTAAACATGAAGATG
upper sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: AT5G40200.1 (Arabidopsis thaliana), 3'ss of exon 2
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttg---ttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
| | || || ||| | | |||||| | | ||||| | | | | | || | | ||| || || |||| ||||||||||||||||| || ||||| ||||| || || |||||||||| ||||||||||| ||||| || ||||||||| | ||||| |||||||
----------------------------------------------------gttggacaacacatttgacatga-tatttttccttatc-tgactagggagttaagggcacttataaaaatgttttctgtttttgtcttttcagATTGATGCAGCTATTAATTCTGGGAATTCTGGTGGTCCTGCATTTAATGATAAAGGAAAATGTGTTGGTATTGCATTTCAGTCTTTGAAACACGAAGATG
upper sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: Vv14s0066g01660.t01 (Vitis vinifera), 3'ss of exon 2
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
|||| || | || ||| | | | | | |||| | ||| ||| |||| || | || | | || || |||||||||| || || || || |||||||| ||||| || || ||||||||| || |||||||| ||||| || |||||||| ||||||||||||||||
----------------------------gtttcatatgt-ttgttacatataaacacactcctttgcctatctaacagga--aaaaaattatgtcttaaacattc-ttgttgttcatga----------gttgcttttgcagATAGATGCTGCAATAAACTCTGGAAATTCTGGTGGACCTGCAATTAATGATAAAGGCAAATGTGTGGGTATCGCATTTCAGTCCCTTAAACATGAAGATG
upper sequence: AC212112.4_FGT002 (Zea mays), 3'ss of exon 2
lower sequence: Vv17s0000g07900.t01 (Vitis vinifera), 3'ss of exon 2
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
| || | | || | | | || |||| | || ||| | | || || | | |||| || | |||||||||| ||||| || || |||||||| ||||| || || || ||||| | ||| || ||||| || || || |||||||||||||||||||||||||
--------------------------------------------gtcatggggtcacatttctccttttt-----ctcttttagttattgttggcttgttgatccatttttctgatgtctcctattcttgatggttttacagATAGATGCTGCTATAAACTCTGGAAATTCTGGTGGGCCTGCCTTCAATGAGAAGGGCAATTGTGTGGGCATTGCATTTCAGTCTCTTAAACATGAAGATGMapped 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|160481372|gb|EY254286.1|EY254286EST: TAGAAATACTTTCATACGTTCATGGTTCTACAGAACTTCTAGGATTGCAG ATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
genomic: TAGAAATACTTTCATACGTTCATGGTTCTACAGAACTTCTAGGATTGCAGgtacattttt ... ttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
EST:
gi|8102677|gb|AW927323.1|AW927323EST: TAGAAATACTTTCATACGTTCATGGTTCTACAGAACTTCTAGGATTGCAG ATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
genomic: TAGAAATACTTTCATACGTTCATGGTTCTACAGAACTTCTAGGATTGCAGgtacattttt ... ttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
EST:
gi|166495282|gb|EG161199.1|EG161199EST: TCATGGTTCTACAGAACTTCTAGGATTGCAG ATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
genomic: TCATGGTTCTACAGAACTTCTAGGATTGCAGgtacattttt ... ttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGAT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.accatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
gtctaat putative branch site (score: 3)
ccttgtctt putative PPT
tctaata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtacattttttttcctgaaattatgataacttcaaataaatctttttataaagatagatgttgcaagtgaagtaactattttgagaaaccatgacttatcggctcaccgacgtgtctaatacgggccttgtcttgttgatagATAGATGCAGCTATTAATTCAGGAAATTCAGGTGGCCCAGCTTTTAATGATAGGGGAAAATGTGTCGGTATAGCTTTTCAGTCTCTTAAACATGAAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG