Sequence
atgc intronic sequence ATGC exonic sequencegcatgttaccttaaacacgttttcacagtactgtgttattgctatgtgatatcgatatagttttctgtatgtgggctgtattgttatcctagtaaaattaattgtttcttccaatcttaatacttgaacttttttccatgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATG
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 7
lower sequence: LOC_Os11g29380.1 (Oryza sativa), 3'ss of exon 7
gcatgttaccttaaacacgttttcacagtactgtgttattgctatgtgatatcgatatagttttctgtatgtgggctgtattgttatcctagtaaaattaattgtttcttccaatcttaatacttgaacttttttccatgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATG
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gtaagttgcctgggacga----tggtagttctgatacatt----tgggctttcttctctgtctta-atgcatgaacatgtttttggttctaatattcaaactgttctcttttaat---aacagttgatttatttgtctcacagACCATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGCAGGCTTCCAAGATACAAGGAAGTGATACTTCTGAATG
upper sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 7
lower sequence: Vv01s0150g00390.t01 (Vitis vinifera), 3'ss of exon 6
gcatgttaccttaaacacgttttcacagtactgtgttattgctatgtgatatcgatatagttttctgtatgtgggctgt--attgttatcctagtaaaattaattgtttcttccaatcttaatacttgaacttttttccatgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATG
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---------------------------------------aaatttttagtttcctttttttccaacctcgctggattatgaaatggagccttaatgaaaaaagttcaaact--caattttggtttacataccttttt----gcagACGATATACAGGAACTATCAAAAACTCACTCTCCAGGAGAGCCCAGGTATCGTGCCAGCAGGTCGTCTTCCTAGATACAAGGAAGTGATACTCTTGAACG
upper sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ17122 (Selaginella moellendorffii), 3'ss of exon 5
gcatgttaccttaaacacgttttcacagtactgtgttattgctatgtgatatcgatatagttttctgtatgtgggctgtattgttatcctagtaaaattaattgtttcttccaatcttaatacttgaacttttttc-catgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATG
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---------------------------------------------------------------------------------------------gtactcgatttcatatttta-tgtacttactttaatctctgagatgtgcagACAATTTACCGGAACTATCAAAAACTAACACTACAAGAAAGCCCTGGAATTGTTCCTGCAGGCAGGCTTCCTCGCTATAAGGAAGTCATACTGCTTGACG
upper sequence: GRMZM2G139894_T01 (Zea mays), 3'ss of exon 7
lower sequence: EFJ31227 (Selaginella moellendorffii), 3'ss of exon 3
gcatgttaccttaaacacgttttcacagtactgtgttattgctatgtgatatcgatatagttttctgtatgtgggctgtattgttatcctagtaaaattaattgtttcttccaatcttaatacttgaacttttttc-catgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATG
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---------------------------------------------------------------------------------------------gtactcgatttcatatttta-tgtacttactttaatctctgagatgtgcagACAATTTACCGGAACTATCAAAAACTAACATTACAAGAAAGCCCTGGAATTGTTCCTGCAGGCAGGCTTCCTCGCTATAAGGAAGTCATACTGCTTGACGMapped 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|87157547|gb|DY402336.1|DY402336EST: CATGCCCTGAATGTCAATCCAAAGGGCCATTCACAGTCAATGTCGAGCAG ACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATT
genomic: CATGCCCTGAATGTCAATCCAAAGGGCCATTCACAGTCAATGTCGAGCAGgcatgttacc ... ttccatgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATT
EST:
gi|21432118|gb|BQ547608.1|BQ547608EST: CATGCCCTGAATGTCAATCCAAAGGGCCATTCACAGACAATGTCGAGCAG ACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATT
genomic: CATGCCCTGAATGTCAATCCAAAGGGCCATTCACAGTCAATGTCGAGCAGgcatgttacc ... ttccatgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctagtaaaattaattgtttcttccaatcttaatacttgaacttttttccatgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATG
tcttaat putative branch site (score: 3)
cttttttccat putative PPT
aaaattaattgtttct 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gcatgttaccttaaacacgttttcacagtactgtgttattgctatgtgatatcgatatagttttctgtatgtgggctgtattgttatcctagtaaaattaattgtttcttccaatcttaatacttgaacttttttccatgcagACTATATATAGGAACTACCAGAAACTCACTCTTCAGGAAAGCCCAGGAATTGTTCCTGCTGGAAGGCTTCCCAGATACAAGGAAGTCATACTTCTGAATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAA