Sequence
atgc intronic sequence ATGC exonic sequence...catgatttcattccgttccatcagaattctggtattatttcttgactcttctattagaagttgaaaagtcaataaccatatattctgctggtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGACTACTCCACCTCCTCGTCTGGCTGACTTTAACTATTCAACTGAAATGTT
Basic information
species | Glycine max |
transcript | GLYMA13G18630.1 |
intron # | 4 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 4
lower sequence: LOC_Os10g33720.1 (Oryza sativa), 3'ss of exon 5
catgatttcattccgttcca-tcagaattctggtattatttcttgactcttc-tattagaagttgaa--aagtcaataaccatatattctgctggtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGACTACTCCACCTCCTCGTCTGGCTGACTTTAACTATTCAACTGAAATGTT
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--tgttctttctttatcatggttaataaacagggctaacagcaagccacaaaatattttaggtcaaagcaaaataaccaagatttttttttttggttct--cagAAATGCACAAAGATGGGGGAACTGGACTGGCTCCTTGGCCTGCTCGATTAACAACTCCACCTCCCCGTCTTGCTGATTTGTATGTCACTGCTGACACATT
upper sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 4
lower sequence: AT3G23300.1 (Arabidopsis thaliana), 3'ss of exon 5
---------catgatttcattccgtt----ccatcagaattctggtattatttcttgactcttct---attagaagttgaaaagtcaata-----acca---tatattctgctggtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGACTACTCCACCTCCTCGTCTGGCTGACTTTAACTATTCAACTGAAATGTT
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gtgagttttcattattctatcttcttttcactaacagagtttcgtcattaacttcacaagcttgtgatattgcatatctgagaacaaatatgctcactaaattatttttcaacgtttctattagATGACCACAAAACCAAGGGAAGTGGATTGGCTCCATGGCCAGCTCGATTAACCTCTCCTCCTCCTCGGCTAGCTGACTTTGGCTATTCCACTGACATTTT
upper sequence: GLYMA13G18630.1 (Glycine max), 3'ss of exon 4
lower sequence: Vv07s0005g03630.t01 (Vitis vinifera), 3'ss of exon 4
catgatttcattccgttccatca--gaattctggtattatttcttgactcttctattagaagttgaaaagtcaataaccatatattctgctggtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGACTACTCCACCTCCTCGTCTGGCTGACTTTAACTATTCAACTGAAATGTT
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-gtg-tttccttgtgctgtattgttgactgttttcactacttcatgagattaacattggaaattgaaaaaatacacgaactaaattttgtcggtcccatcagAAAACCATCAAACAAGAGGTAGTGGATTGGCTCCTTGGCCAGCTCGATTAACTGCTCCTCCTCCTCGTCTAGCTGATTTTGGCTATACCAGTGACATGTTMapped 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|18692800|gb|BM521648.1|BM521648EST: TGCTGTTTGGGGAGTTAAAATGAAAGCTTGTATCACACGCTATTCTGATC AGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGA
genomic: TGCTGTTTGGGGAGTTAAAATGAAAGCTTGTATCACACGCTATTCTGATCgtgagtgata ... gtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGA
EST:
gi|19269829|gb|BM886085.1|BM886085EST: TGCTGTTTGGGGAGTTAAAATGAAAGCTTGTATCACACGCTATTCTGATC AGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGA
genomic: TGCTGTTTGGGGAGTTAAAATGAAAGCTTGTATCACACGCTATTCTGATCgtgagtgata ... gtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ctcttctattagaagttgaaaagtcaataaccatatattctgctggtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGACTACTCCACCTCCTCGTCTGGCTGACTTTAACTATTCAACTGAAATGTT
caataac putative branch site (score: 2)
aataaccatatatt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
catgatttcattccgttccatcagaattctggtattatttcttgactcttctattagaagttgaaaagtcaataaccatatattctgctggtctatgcagAGATGCACAGAGCAAAAGGAGCTGATTTGGCTCCTTGGCCAGCTCGATTGACTACTCCACCTCCTCGTCTGGCTGACTTTAACTATTCAACTGAAATGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC
catgatt
- - - -tcattcc
- - - - - - - - tccatca
- - - - - - - - - - - - -attctgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttctgct