Sequence
atgc intronic sequence ATGC exonic sequencegtatgctttcacttctcactgtgctgcagttggaagttgcaacgctgcatgcatatcaagtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA
Basic information
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 5
lower sequence: LOC_Os08g25734.2 (Oryza sativa), 3'ss of exon 5
gtatgctttcacttct--cactgtgctgcagttggaagttgcaacgctgcatgcatatcaagtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA
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gtatgctttcaatttttacaccttgctgtggctgaagattatggaatttgaagcatgtgaatttata--------attgtctccttatgatataaaatataccatcaaaatatctgcagTTTCTATGACCGGTCTGCTCCAATTTATACACAACCTCGACACTTGCCTCCTTCGAAGGTTCTTGATGCTGATGTGACAGACAGTGTCATTGGTGAAGGT
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA02G47460.1 (Glycine max), 3'ss of exon 5
gtatgctttcacttctcactgtgctgcagttggaagttgcaacgctgcatgcatatcaa--gtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA
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------gtaaattatataggctatttaatatatccatcatattgacaaatgtatttcaacggtagtatattgtggttctgatgtttatgtgttcatgcattttggcatattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 5
lower sequence: GLYMA14G01290.1 (Glycine max), 3'ss of exon 5
gtatgctttcacttctcactgtgctgca-gttggaagttgcaacgctgcatgcatatcaagtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA
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gtaaattgcctatttgatatatccatcatattgacaaatgtatttcaatg-----atagtgttttgtggttctgat--gtttatg-tgttcatgcgttttggc--atattgattgcagTTTCTATGATCGTTCATCTCCAATCTACACCCAACCACGATATTTGCCTCCCTCTAAGATGCTTGATGCTGATGTCACTGATAGTGTTATTGGTGAAGGA
upper sequence: GRMZM2G068506_T03 (Zea mays), 3'ss of exon 5
lower sequence: Vv12s0057g01480.t01 (Vitis vinifera), 3'ss of exon 5
gtatgctttcacttctcactgtgctgca-gttggaagttgcaa-cgctg-----catgcatatcaagtcttacaatttcaat-tagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA
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--gtagttttacagcccatcagactgtatactgtgaattttgatctctgttcaacagtttctttcattaccacatttctgatgcagtttatgata--ttaatatggttttgaacttaaattgcagCTTCTACGACCGTTCCTCTCCAATCTACACCCAACCTCGATATTTGCCCCCATCTAAGATGCTTGATGCTGATGTAACCGATAGTGTTATTGGTGAGGGCMapped 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|56691604|gb|CX129507.1|CX129507EST: TTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATGCCAGATTTCAG CTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACC
genomic: TTTTATAATGCAAACTTGGGAATAACCAAGAAGCCAATACCAGATTTCAGgtatgctttc ... ctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACC
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA
tactgat putative branch site (score: 2)
atttcaatta 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgctttcacttctcactgtgctgcagttggaagttgcaacgctgcatgcatatcaagtcttacaatttcaattagttcctactgatttagtgttccccttaaatctgaatacagCTTCTATGACCGTTTTGCTCCAATTTATACACAACCTCGACACCTGCCACCTTCAAAGGTTCTTGATGCTGATGTGACAGACAGTGTTATTGGTGAAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT