Sequence
atgc intronic sequence ATGC exonic sequencegtaagcttatcataaatatatgtgcaaaatattgaaatgatgaatagtttgtgatgtttgtaactggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG
Basic information
species | Glycine max |
transcript | GLYMA14G37520.1 |
intron # | 28 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 28
lower sequence: LOC_Os05g07130.2 (Oryza sativa), 3'ss of exon 17
--------------------------------------------------gtaagcttatcataaatatatg-----tgcaaaatat-tgaaatgatgaat----agtttgtgatgtttg--taa-ctggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG
|| || || ||| | ||| || ||| | ||| | || | ||| | | || ||| || ||| ||| ||||||||||| || || || ||| | ||||||||||||||| ||||||| ||||| || ||||||
gtacgtaatctcttgattgaattgcattgtttctagaggcaacttcttatgtcagtatagcatttggagatgaagactgtaaaggagatgagctaatagagtgagagtctctcatttttaattattctgatgtttagATATGGACCAGCACGCTTCAGAGGACAATTTTGACAGCAAGTCCAATAGTTGGATTCCCAAAG
upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 28
lower sequence: GRMZM2G021846_T02 (Zea mays), 3'ss of exon 17
gtaagcttatcataaatatatg-tgcaaaatattgaaatgatga-atagtttgtgatgtttgtaactg-----gtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG-------------------------------------
||||| | | | || | || || | | || | || | || | |||| || | ||| ||||||||||| ||||| || ||| ||||||||||||||||| ||||||||||||| || || |||
gtaagtattttcccatgatttaatgatggatctgaccagcataacatgggctgaaa-atttgcaattatcgaattgtttagATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAGGTATTTGGTTACACGATTTAGGAGTCTTCTTAAAGAA
upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 28
lower sequence: GRMZM2G021846_T01 (Zea mays), 3'ss of exon 17
gtaagc-ttatcataaatatatgtgcaaaatattgaaatgatga-atagtttgtgatgtttgtaact-----ggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG
||||| || || | | || || | | || | || | || | |||| || | ||| ||||||||||| ||||| || ||| ||||||||||||||||| ||||||||||||| || || |||
gtaagtattttcccatgatttaatgatggatctgaccagcataacatgggctgaaa-atttgcaattatcgaattgtttagATATGGACCAGTACCCTTCAGAGAACAATTTTGACAGCAAGTCCAATTGTTGGATTCCCCAAG
upper sequence: GLYMA14G37520.1 (Glycine max), 3'ss of exon 28
lower sequence: Vv06s0004g06920.t01 (Vitis vinifera), 3'ss of exon 17
------------------------gtaagcttatcataaatatatgtgcaaaatat--tgaaatgatgaatagt-ttgtgatgtttgtaactggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG
| | ||| || ||||| ||| | | ||| | | || || | || || | ||| || |||||||||||||| ||||||||| |||||||||| || ||| |||||||||||||||| ||||||
taatgctttatactattctactagttgaatatatatggaagtcatgtgtaaattttaacagaattctaataagcattcttgtgattttg-ctgtggtttagATATGGACTAGCACACTGCAGAGAACAATTTTAACGGCAAGTCCAATTGTTGGGTTCCCAAAGMapped 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|193519728|gb|FK476263.1|FK476263EST: AGCTTGCCAAATTTGTTGAAAAGCGTCTCAAATCAGAACGAGCTGCATGT ATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTT
genomic: AGCTTGCCAAATTTGTTGAAAAGCGTCTCAAATCAGAACGAGCTGCATGTgtaagcttat ... tggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTT
EST:
gi|193308294|gb|FK277299.1|FK277299EST: AGCTTGCCAAATTTGTTGAAAAGCGTCTCAAATCAGAACGAGCTGCATGT ATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTT
genomic: AGCTTGCCAAATTTGTTGAAAAGCGTCTCAAATCAGAACGAGCTGCATGTgtaagcttat ... tggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTT
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atgtgcaaaatattgaaatgatgaatagtttgtgatgtttgtaactggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG
ttgtaac putative branch site (score: 2)
aaaatattgaaatgat 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtaagcttatcataaatatatgtgcaaaatattgaaatgatgaatagtttgtgatgtttgtaactggtgtctagATATGGACTAGTACACTGCAGCGAACAATTTTGACAGCAGGTCCAATTGTTGGGTTTCCAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGCAG