Sequence
atgc intronic sequence ATGC exonic sequencegtaactacacctgtcttgcttatcttttgtatgtatacctgtgaatgatatagagttatggtactaagacatgtagattgatgtttctatgacagGAGGTATAGTGAACAACGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA
Basic information
species | Arabidopsis thaliana |
transcript | AT5G57610.1 |
intron # | 8 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G039106_T02 (Zea mays), 3'ss of exon 6
gtaactacacctgtcttgcttatctt--ttgtatgtatacctgtgaatgatataga-gttatggtactaagacatgtagattg--atgtttctatgacagGAGGTATAGTGAACAACGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA
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gattttttgttgagtttttgaatcttagtcataaatatattgcctaggcttattgttattatgtcgcagaaatgattaggttgcaatacattttctctagGGGCCATTGTAAACGATTCCTTACGCCCTCAAATCCCTTCATGGTGTGATCCTGAGTGGAAGGGATTGATGGAAAGCTGTTGGTCCAGTGATCCAGCGGA
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G039106_T03 (Zea mays), 3'ss of exon 6
--gtaactacacctgtcttgcttatcttttgtatgtatacctgtgaatgatatagagttatggtactaagacatgtagattgatg----tttctatgacagGAGGTATAGTGAACAA--CGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA
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cattttctctaggggccattgtaaacgattcctt--acgccctcaaatcccttcatggtgtgatcctgagtggaagggattgatggaaagctgttggtccagTGATCCAGCGGAGAGACCGTCCTTCACTGATATATCTCAAAG-GTTGAGGAAAATGGCCGCTGCAATGAATGTGAAGTGAAGGTTCGGAAGCCATATTTGT
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G052658_T01 (Zea mays), 3'ss of exon 7
----gtaactacacctgtcttgcttatcttttgtatgtat-acctgtgaatgatatagagttatggtactaagacatgtagattg--atgtttctatgacagGAGGTATAGTGAACAACGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA
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atttatgttgatttttgaatctttagtcataaatatatctcgcctaggcttgttgtta--ttatgtcacagtagtgatctgattgcaatgccttttttctagGGGGCATTGTAAACGATTCCCTACGTCCTCAAATTCCTTCATGGTGTGATCCTGAGTGGAAGGGATTGATGGAAAGCTGTTGGTCCAGTGATCCAGCTGA
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G450602_T01 (Zea mays), 3'ss of exon 2
----gtaactacacctgtcttgcttatcttttgtatgtat-acctgtgaatgatatagagttatggtactaagacatgtagattg--atgtttctatgacagGAGGTATAGTGAACAACGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA
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atttatgttgatttttgaatctttagtcataaatatatctcgcctaggcttgttgtta--ttatgtcacagcagtgatctgattgcaatgccttttttctagGGGGCATTGTAAACGATTCCCTACGTCCTCAAATTCCTTCATGGTGTGATCCTGAGTGGAAGGGGTTGATGGAAAGTTGTTGGTCCAGTGATCCAGCTGA
upper sequence: AT5G57610.1 (Arabidopsis thaliana), 3'ss of exon 8
lower sequence: GRMZM2G374044_T01 (Zea mays), 3'ss of exon 2
----gtaactacacctgtcttgcttatcttttgtatgtat-acctgtgaatgatatagagttatggtactaagacatgtagatt--gatgtttctatgacagGAGGTATAGTGAACAACGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA
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atttatgttgatttttgaatctttagtcataaatatatctcgcctaggcttgttgtta--ttatgtcacagcagtgatctgattacaatgccttttttctagGGGGCATTGTAAACGATTCCCTACGTCCTCAAATTCCTTCATGGTGTGATCCTGAGTGGAAGGGGTTGATGGAAAGCTGTTGGTCCAGTGATCCAGCTGAMapped 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|124825253|gb|EH910119.1|EH910119EST: ACTCACTGGTGAAGAACCATACGCAGACATGCATTGTGCTTCCATAATTG GAGGTATAGTGAACAACGCATTGCGTCCAAAAA
genomic: ACTCACTGGTGAAGAACCATACGCAGACATGCATTGTGCTTCCATAATTGgtaactacac ... tctatgacagGAGGTATAGTGAACAACGCATTGCGTCCAAAAA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgaatgatatagagttatggtactaagacatgtagattgatgtttctatgacagGAGGTATAGTGAACAACGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA
gattgat putative branch site (score: 4)
tgtttct CT-rich tract
tgatata 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaactacacctgtcttgcttatcttttgtatgtatacctgtgaatgatatagagttatggtactaagacatgtagattgatgtttctatgacagGAGGTATAGTGAACAACGCATTGCGTCCAAAAATCCCACAGTGGTGTGATCCAGAGTGGAAGGGATTGATGGAAAGTTGCTGGACGTCTGAGCCAACAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA