Sequence
atgc intronic sequence ATGC exonic sequence...tgcaattttaattgtttcccaatcaaaattagaattgcataagtcttgttctataatttttataaagaaggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTTGAGATGGTTCATAGTT
Basic information
species | Glycine max |
transcript | GLYMA04G38560.1 |
intron # | 2 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os11g08210.1 (Oryza sativa), 3'ss of exon 2
-tgcaattttaattgtttcccaatcaaaattagaattgcataagtcttgttctataatttttataaagaaggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTTGAGATGGTTCATAGTT-
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ccaaaaactttttaccaccaccactcgcatgcattccacatcaatcttgatc-actttgctaataatttcagttttttttttggttaatttttttttgcagTTGGATGATTGGGTGTTGTGCCGAATCTACAACAAGAAGGGAGTGATCGAGAGGTACGACACGGTGGACGCCGGCGAGGACGTGAAGCCGGCG-GCGGCGG
upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 2
lower sequence: LOC_Os05g34830.3 (Oryza sativa), 3'ss of exon 1
tgcaattttaattgtttcccaatcaaaattagaattgcataagtcttgttctataatttttataaagaaggatctgatttt-gttgtgttatggtgc-acagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTT--GAGATGGTTCATAGTT
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-ttaattgggcggatttcatcat-atatttattgttgtgatcacgaaatgatatggtcttgatgaaatttgatttgatttttggtggtttgtgttattgcagCTAGATGATTGGGTCCTGTGCCGAATCTACAACAAGAAAGGCGGCGTGGAGAAGCCGAGCGGCGGCG--GCGGCGGCGAACGTTCGAATATGATGAGCCACG
upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 2
lower sequence: GRMZM2G180328_T01 (Zea mays), 3'ss of exon 2
tgcaattttaattgtttcccaatcaaaattagaattgcataagtcttgttctataatttttataaagaaggatctgattttg--ttgtgttatggtgc-acagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCG-CAGCGAAGATGAATGTTG-AGATGGTTCATAGTT
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---aaatcgtataattgttctacctttttgttggatggatagatttggtggtatgggcgtgattaagatttttttcctctcggttttttttttgctgttgcagTTGGATGATTGGGTGCTGTGCCGAATCTACAACAAGAAAGGCGCGCTGGAGAAGCCGACCGGAGCCGGCGGCAGGGCCGAGGCCAGCAGCCAGGGCGCGC--
upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G08790.1 (Arabidopsis thaliana), 3'ss of exon 2
tgcaattttaattgtttcccaatcaaa--attagaattgcataagtcttgttctataatttttataaagaaggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTTGAGATGGTTCATAGTT
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-gtaagttctgtttcttattaacttatgtatcatcttttcgtgaatgatgattta-gattatta---------actttgttgtggtgggttttgctgtacagCTTGATGATTGGGTTTTATGTCGAATATACAACAAGAAAGGAACCATGGAGAAGTATTTCCCCGCGGATGAGAAGCCGAGGACCACGACAATGGCTGAAC
upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 2
lower sequence: AT5G63790.1 (Arabidopsis thaliana), 3'ss of exon 2
tgcaattttaattgtttcccaat--caaaattagaattgcataagtcttgttctataatttttataaagaaggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTTGAGATGGTTCATAGTT
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-gtaagcttttctgatttttaatttctgggttttttttcgatttttgtgatgatgatgaattgatgatgattaatgggttttttttggttgaaattttgcagCTTGATGATTGGGTTTTGTGTCGGATATACAATAAGAAAGGAACAATGGAGAAGTATTTACCGGCGGCGGCTGAGAAACCGACGGAAAAGATGAGTACGT
upper sequence: GLYMA04G38560.1 (Glycine max), 3'ss of exon 2
lower sequence: Vv07s0031g02610.t01 (Vitis vinifera), 3'ss of exon 2
-tgcaattttaattgtttcccaatcaaaattagaattgcataagtcttgttctataatttttataaagaag-gat--ctgattttgttg--------tgttatgg--tgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTTGAGATGGTTCATAGTT-----
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gtacgattgtaatt-----ctatactacattaaagatatttatttattatttaaaaaaaaaagaaaaagagtgatggttctttttattgatatatattattattgactttgcagCTTGACGATTGGGTCTTATGTCGAATATACAACAAGAAAGGCAGCGCCGAGAAACAGCACACCTTTG-ATCAAAAGTCAAT---GAAATA-TCCAGAACTTGAAGMapped 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|120533637|gb|EH261770.1|EH261770EST: TCGCCAATGTTGACCGATCTGCCTCCAAGNNNNNNNNCAACAACTTGAGG CTTGATGATTGGGTGTTGTGTCGAATCT---ACAAGAAAGGGAAGATTGAG
genomic: TCGCCAATGTTGACCGATCTGCCTCCAAGAAAAAAAACAACAACTTGAGGgtatgtccca ... tggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttgttctataatttttataaagaaggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTTGAGATGGTTCATAGTT
atctgat putative branch site (score: 4)
tataatttttataaag 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
tgcaattttaattgtttcccaatcaaaattagaattgcataagtcttgttctataatttttataaagaaggatctgattttgttgtgttatggtgcacagCTTGATGATTGGGTGTTGTGTCGAATCTACAACAAGAAAGGGAAGATTGAGAAATACAACACAGGCGCAGCGAAGATGAATGTTGAGATGGTTCATAGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATG
- - - - - - - - - ccaatca
- - - - - - - - - - - - - - - - - -tgcataa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataaagaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgttgtg