Sequence
atgc intronic sequence ATGC exonic sequence...tacttctagattataatgattagaacatggtgaagtcaagtttattgttgttgcctgggtagctagtttgttgatttcactttgcctttgccatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC
Basic information
species | Glycine max |
transcript | GLYMA09G25090.1 |
intron # | 1 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA09G25090.1 (Glycine max), 3'ss of exon 1
lower sequence: LOC_Os03g01660.1 (Oryza sativa), 3'ss of exon 2
--------------tacttctagattataatgattagaaca---tggtgaagtcaagtttattgttgtt--gcctgggtagctagtttgttgatttcactttgcctttgccatg--ctta-----gATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC
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gtatgacccctatgcatttctagatcataactattttttctgtttattggaggggaaacaattgttctccagccttatcagctattcatttggttccaatttaatttcattgtgaactcacagGCGTTGAAGAGTTATATTTGGCTTCAGTGCTTTGATGGTTCCATACAACAAGTGGAGGAGGAGGTTGCCATGTTTTGCCCTATGATATGTCGAGAGATAG---
upper sequence: GLYMA09G25090.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G109725_T04 (Zea mays), 3'ss of exon 3
tacttctagattataatgattagaacatggtgaagtcaagtttattgttgttgcctgggtagctagtttgttgatttcactttgcctttgccatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC
|||| | |||| | | | | | | | ||||| | | || || ||| | || | || || | | || | || ||||||||||| | |||||||| ||||||||||| ||||| ||||| || ||||| ||||||||||| || | ||| |
-gtaattagagggaagcaattac--ttttccaatcttatgcggttcaattcagcctgtcttg--agcttattggtggtg----aactataacagGCGT---TAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
upper sequence: GLYMA09G25090.1 (Glycine max), 3'ss of exon 1
lower sequence: GRMZM2G109725_T03 (Zea mays), 3'ss of exon 2
-------------tacttctagattataatgattagaacatggtgaagtcaagtttattgttgt-tgcctgggtagctagtttgttgatttcactttgcctttgccatgcttagA--TGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC
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gtacaatcccctgcagcccccctctccggtaattagagggaagcaattacttttccaatcttatgcggttcaattcagcctgtcttgagcttattggtggtgaactataacagGCGTTAAAGACTTATATCTGGCTTCAGTGCTTTGATGGTTCCATTCAGCAAGTGGAGGAGGAGGTTGCAATGTTCTGCCCCATGATATGTCGTGAAATTG---
upper sequence: GLYMA09G25090.1 (Glycine max), 3'ss of exon 1
lower sequence: Vv16s0050g00720.t01 (Vitis vinifera), 3'ss of exon 2
tacttctagattat--aatgattagaacatggtgaagtcaagtttattgttgttgcctgggtagctag-tttgttgatttcactttgcctttgccatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC
| ||| ||| | || | ||| || | || || | | || | | | | ||| || |||| || || | ||||||| || || |||||||| ||||||| |||||||||||||| ||||| || |||||||| |||||||||||||||||||| |||| ||| ||||||
-tttgataggctatttggtttttgttatatgatgtactcttattcactctttatccttttcttatggcctttatttattttgtttaaaatt--gtgtatcaagATGAAGTCTTATATCTGGCTCCAAACTGCTGATGGTTCTATTCAACAAGTTGAAGAAGAGGTTGCCATGTTTTGCCCCATGATATGCCGAGAAATACTTCMapped 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|15203134|gb|BI425902.1|BI425902EST: ATGTCTGATGCTGCTATGGCAGTTGTGAAACCTGAG ATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTA
genomic: ATGTTTGATGCTGCTATGGCAGTTGTGAAACCTGAGgtatggtatt ... ccatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTA
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.tgttgttgcctgggtagctagtttgttgatttcactttgcctttgccatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC
tgttgat putative branch site (score: 4)
cctttgcc putative PPT
ttgattt 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tacttctagattataatgattagaacatggtgaagtcaagtttattgttgttgcctgggtagctagtttgttgatttcactttgcctttgccatgcttagATGAAATCCTACATCTGGCTTCAAACTGTGGATGGTTCTATTCAGCAAGTAGAGGAAGAGGTAGCCATGTTTTGCCCCATGATTTGCCAGGAAGTACTTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- cttctag
- - - - - - - - - - - - -catggtg
- - - - - - - - - - - - - - - - - - - - - - - - tgttgcc