Sequence
atgc intronic sequence ATGC exonic sequencegtatgagttttgagtccttaactgttttttttttcttatcatatctccagaatataattaaaactctgactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG
Basic information
species | Arabidopsis thaliana |
transcript | AT1G19650.2 |
intron # | 6 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA06G03300.1 (Glycine max), 3'ss of exon 7
---gtatgagttttgagtccttaactgttttttttttcttatcatatctccagaatataattaaaactctgactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG
| | || | || | | | |||| | |||| | ||| | |||| ||| |||| | || || |||| |||||||||| ||| | | ||||| ||||||||||| |||||| || ||||||||||| |||||||||||||| ||| ||||| | | || |||||
gtaacactacattcaattctgttaacggagttttctctcaatcaactagttttgttatt-tgaaaattctaactaa--ccgtaagtt-ctcagTGAGCTGCCAGAATTTCTTGCTGGTAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA04G03230.1 (Glycine max), 3'ss of exon 6
---gtatgagttttgagtccttaactgttttttttttcttatcatatctccagaatataattaaaactctgactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG
| || | || | | || |||| | |||| | ||| | |||| |||||||| || || || |||| |||||||||| ||| | ||||| | ||||||||||| |||||| || ||||||||||| |||||||||||||| ||| ||||| | | || |||||
gtaactctacattcaattctgttaatggagttttctctcaatcaactagtttagttatt-tgaaaattctgactaa--ctgtaagtt-ctcagTGAGCTGCCAGAATTTCTTGGTGGCAGTTGCACTTGTGTAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAAGACCCAAACATTTTAAAG
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA17G37150.1 (Glycine max), 3'ss of exon 7
--------gtatgagttttgagtccttaactgttttttttttcttatca-tatctccagaatataatt--aaaactctgactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG
| || | |||| || | | ||| || |||||| | | | | ||| ||| ||||||||| | | ||||| ||| ||||||| || ||| | ||||||| |||||||||| |||||| || ||||||||||| |||||||||||||| ||| | || | | || |||||
gtaactatgcattaattttt-gttaatggtgttatttacttatttatcaatcagcttgtattgttatttggaaattctgactatctgcgtggtttgtttagCAAGCTGCCTGAATTTCTAGGTGGTAGTTGCACTTGTATAGATCAAGGTGGTTGTATGAGGTCTGATAAAGGGCCATGGCAGGATCCAAACATTTTAAAG
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: GLYMA14G07850.1 (Glycine max), 3'ss of exon 7
----gtatgagttttgagtccttaactgttttttttttcttatcatatctccagaatataattaaaactctgactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG
|||| | | |||| | || ||| || |||| | | | | | ||| ||||||||| | | || |||||| ||||||| || ||| | ||||||| |||||||||| |||| || |||||||||||||||||||||||||| ||| | || | | || |||||
gtaactatgcaataatttttgttaatggcgttatttatca-atca-gtttgtattgttatttggaaattctgactatctgcgtggttt-ttcagCGAGCTGCCTGAATTTCTAGGTGGTAATTGCACTTGTATGGATCGAGGTGGTTGTATGAGATCTGATAAAGGGCCATGGCAGGATCCAAACATTTTAAAG
upper sequence: AT1G19650.2 (Arabidopsis thaliana), 3'ss of exon 6
lower sequence: Vv18s0001g12950.t01 (Vitis vinifera), 3'ss of exon 7
gtatgagtt---ttgagtccttaact-gttttttttttcttatcatatctccagaatataattaaaactct-gactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG
||| || || || | ||| || ||| || | | || | | ||| ||| || |||||| | | || | || || |||| || ||| ||||||||| || | ||||||||||||||||||||| ||| |||||||| ||||| |||||||| | | ||| |||||
--gtgaattcttttctgtattggactcaccacttattttgcattcaagcctactaactttttgaaatttcttgaatatattggtgattt-cttagTGAGTTGCCCGAATTTCTCGGTGGTAGCTGTATCTGTGCAGATCAGGGAGGTTGTTTGAAGTCTGATAAGGGGCCGTGGAAAGATCCAAACATATTAAAGMapped 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|86088306|gb|DR384065.1|DR384065EST: GTCCTTGGGAACAAGTACCAGAACAAATTACTTGAGATGATTGATGCAAG CCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGG
genomic: GTCCTTGGGAACAAGTACCAGAACAAATTACTTGAGATGATTGATGCAAGgtatgagttt ... acttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGG
EST:
gi|124909165|gb|EH983245.1|EH983245EST: AACAAATTACTTGAGATGATTGATGCAAG CCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGG
genomic: AACAAATTACTTGAGATGATTGATGCAAGgtatgagttt ... acttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGG
atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.ttatcatatctccagaatataattaaaactctgactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG
ctctgac putative branch site (score: 3)
cttgttc putative PPT
aatataattaaaactc 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
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
gtatgagttttgagtccttaactgttttttttttcttatcatatctccagaatataattaaaactctgactatatttggaacttgttcagCCAGCTGCCAGATTTTTTCGGTGGTACTTGCACTTGTGCAGATCAGGGAGGTTGTATGAGATCTGATAAAGGGCCCTGGAAAGACTCTGAGATACTAAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGATC