RetrogeneDB ID: retro_atha_14

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 5:21167431..21169462(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT5G52090
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT5G37150
• Aliases: None
• Description: None

Sequence

>retro_atha_14
ATGACTTTAACAACAAACACTCGAATTTGGAATGCTTTGCACAACGAAGCTGACATATCGACTCTAACCAAGAGTGTGCT
TCAGGCTAATACTGAGGGTACAGAACAATGTTTTTGTTCTGAAAATGATGGGAGATCTGACCTTGTTTTGGATATAATCC
GTTCAACGAAATTGAACTCTTCCCAAGAGGATGCAATCTTGGGCTGCCTTGAGACAAGAAACTGTACCCATAAGAACAGT
GTGAAACTGATATGGGGACCTCCTAGAACAGGCAAAACAAAGACGGTCGCGACTCTTCTCTTTGCCCTTCTCAAACTAAG
GTGCAAGACAGTTGTGTGTGCTCCTACAAACACAGCTATTGTACAAGTTACATCAAGGCTCTTATCCTTATTTAAGGAAA
ACTCGACAGCGGAAAATGCTACTTACAGGCTAGGGAATATCATTTTATCCGGAAACCGGGACAGAATGGGGATTAACAAG
AACGATCATGTTCTTCTCGATGTGTTTCTTGATGAGCGTATTGGTAAGCTTGGTAAACTGTTTTCACCATTTTCTGGATG
GATGCAGAGATTAGAGTCACTGATACAGTTTCTTGAAAACCCCGAGGGAAAGTATGAGAGACATGTCTACGAGTTAGAAG
AAGTTGAAAGAATGAATGAAGAAGATGAAAGGGAAGAAGTTGTTGTTAACATTCCTACTTTTGGAGAATTCGTTCAGAAG
AATTTTAATAGCTTAAGTGAAGAAGTGAAGACATGCATCGTTGATTTGTATACACATCTTCCCAAGGTTTACCTTCCATA
TGAAGATGTGAAGAAAATGATTGCTTCTCGTCAAACTCTTCAGCGTATCAGATATTTCTTGAGGGAGAATTCTTCTAGGG
TTGATTTCGAGGAAGGAAATTTCAGATTTGATTGCTTCAAAAGACTCAGTGATGATTGCCTCAAGGCTCTACGCTTACTT
CCAAAACGTTTTGAGATTCCAGACATGTTAGAAAACGAAGATATTAGGAAATTTTGTCTTCAAAACGCGGATATTATCCT
CTGCACAGCCTCGGGTGCTGCGGAAATGAACGTGGAAAGGACAGGAAATGTAGAACTGCTTGTGGTTGATGAGGCGGCTC
AGCTTAAGGAATGTGAATCAGTTGCTGCATTGCAACTTCCGGGACTGCGTCACGCCATTTTAATAGGAGATGAGTTTCAA
TTGCCTGCAATGGTTCATAATGAGATGTGTGAAAAGGCGAAATTCGGAAGAAGCTTGTTTGAGAGATTGGTTTTGCTTGG
TCACAACAAACACTTGCTTGATGTTCAATATCGAATGCATCCTTCTATTAGTCGTTTCCCCAACAAGGAGTTTTATGGTG
GGAGAATCAAAGATGCTGAAAATGTTAAAGAAAGTATTTATCAAAAGAGGTTTCTTAAAGGAAACATGTTTGACTCATTT
TCTTTTATCAATGTTGGACGTGGAAAAGAAGAGTTTGGTGATGGACATAGTCCCAAAAACATGGTTGAAGTTGCTGTCAT
TTCTGAAATTATATCAAATCTTTACAAAGTTTCATGTGAAAGGAGGATGAAGGTGAGTGTCGGAGTGGTCTCACCTTACA
AAGGACAGATGAGAGCAATCCAAGAGAAAATCGGAGATAAGTACAGTTCCTTATCAGGTCAGCAATTCACTTTGAATGTT
CGGTCCGTAGATGGTTTTCAAGGAGGAGAAGAAGACATTATCATCATCTCCACCGTTAGAAGTAACGGTAATGGAAAAGT
CGGATTTCTTAACAACCGTCAAAGAGCTAACGTGGCACTGACTCGAGCAAGACACTGTTTATGGGTGATTGGGAACGAGA
CAACTTTGGCTCTAAGTGGTTCGATTTGGGCAACACTGATAAGTGAGTCTAGGACACGTGGATGTTTCCATGATGCTACT
GATGAGATGAATCTAAGAGATGCCATGAATGAAGCTTTGCTTGAGGATGTGTCTTCGAGTCTTGGATCTCTTTCGCTTAG
GAATGGCCATGGAAGAAGAAATGTTTGGTAG

Alignment

ORF - retro_atha_14 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.08 %
• Parental protein coverage: 80.33 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTLTTNTRIWNALHNEAAISTLTKSVLQANT--VNNVFVLKMMGDLTLFLDIIRSTKLNSSQEDAILGCL
          MTLTTNTRIWNALHNEA.ISTLTKSVLQANT......F.....G...L.LDIIRSTKLNSSQEDAILGCL
Retrocopy MTLTTNTRIWNALHNEADISTLTKSVLQANTEGTEQCFCSENDGRSDLVLDIIRSTKLNSSQEDAILGCL

Parental  ETRNCTHKNSVKLIWGPPGTGKTKTVATLLFALLKLRCKTVVCAPTNTAIVQVASRLLSLFKENSTSENA
          ETRNCTHKNSVKLIWGPP.TGKTKTVATLLFALLKLRCKTVVCAPTNTAIVQV.SRLLSLFKENST.ENA
Retrocopy ETRNCTHKNSVKLIWGPPRTGKTKTVATLLFALLKLRCKTVVCAPTNTAIVQVTSRLLSLFKENSTAENA

Parental  TYRLGNIILSGNRDRMGIHKNDHVLLDVFLDERIGKLGKLFSPFSGWMQRLESLIQFLENPEGKYERHVY
          TYRLGNIILSGNRDRMGI.KNDHVLLDVFLDERIGKLGKLFSPFSGWMQRLESLIQFLENPEGKYERHVY
Retrocopy TYRLGNIILSGNRDRMGINKNDHVLLDVFLDERIGKLGKLFSPFSGWMQRLESLIQFLENPEGKYERHVY

Parental  ELEEVERMEEEAERQEVVVNIPTIGEFVKKNFNSLSEEVETCIVDLFTHLPKVYLPYDDVKIMIASRQSL
          ELEEVERM.EE.ER.EVVVNIPT.GEFV.KNFNSLSEEV.TCIVDL.THLPKVYLPY.DVK.MIASRQ.L
Retrocopy ELEEVERMNEEDEREEVVVNIPTFGEFVQKNFNSLSEEVKTCIVDLYTHLPKVYLPYEDVKKMIASRQTL

Parental  QRIRYFLRENSSRVDFEEGNFRFDCFKRLSVDCLKALRLLPKRFEIPDMLENEDIRKFCLQNADIILCTA
          QRIRYFLRENSSRVDFEEGNFRFDCFKRLS.DCLKALRLLPKRFEIPDMLENEDIRKFCLQNADIILCTA
Retrocopy QRIRYFLRENSSRVDFEEGNFRFDCFKRLSDDCLKALRLLPKRFEIPDMLENEDIRKFCLQNADIILCTA

Parental  SGAAEMNVERTGNVELLVVDEAAQLKECESVAALQLPGLRHAILIGDEFQLPAMVHNEMCEKAKFGRSLF
          SGAAEMNVERTGNVELLVVDEAAQLKECESVAALQLPGLRHAILIGDEFQLPAMVHNEMCEKAKFGRSLF
Retrocopy SGAAEMNVERTGNVELLVVDEAAQLKECESVAALQLPGLRHAILIGDEFQLPAMVHNEMCEKAKFGRSLF

Parental  ERLVLLGHNKHLLDVQYRMHPSISRFPNKEFYGGRIKDAENVKESIYQKRFLQGNMFGSFSFINVGRGKE
          ERLVLLGHNKHLLDVQYRMHPSISRFPNKEFYGGRIKDAENVKESIYQKRFL.GNMF.SFSFINVGRGKE
Retrocopy ERLVLLGHNKHLLDVQYRMHPSISRFPNKEFYGGRIKDAENVKESIYQKRFLKGNMFDSFSFINVGRGKE

Parental  EFGDGHSPKNMVEVAVVSEIISNLFKVSCERRMKVSVGVVSPYKGQMRAIQEKIGDKYSSLSGQQFALNV
          EFGDGHSPKNMVEVAV.SEIISNL.KVSCERRMKVSVGVVSPYKGQMRAIQEKIGDKYSSLSGQQF.LNV
Retrocopy EFGDGHSPKNMVEVAVISEIISNLYKVSCERRMKVSVGVVSPYKGQMRAIQEKIGDKYSSLSGQQFTLNV

Parental  RSVDGFQGGEEDIIIISTVRSNSNGKVGFLNNRQRANVALTRARHCLWVIGNETTLALSGSIWATLISES
          RSVDGFQGGEEDIIIISTVRSN.NGKVGFLNNRQRANVALTRARHCLWVIGNETTLALSGSIWATLISES
Retrocopy RSVDGFQGGEEDIIIISTVRSNGNGKVGFLNNRQRANVALTRARHCLWVIGNETTLALSGSIWATLISES

Parental  RTRGCFYDATDEMNLRNAMNEALLEDVSSSLGSLSIRNGHGRRNVW
          RTRGCF.DATDEMNLR.AMNEALLEDVSSSLGSLS.RNGHGRRNVW
Retrocopy RTRGCFHDATDEMNLRDAMNEALLEDVSSSLGSLSLRNGHGRRNVW

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Arabidopsis thaliana was not studied using RNA-Seq expression data.

ChIP-Seq

Arabidopsis thaliana was not studied using ChIP-Seq data.

EST

Arabidopsis thaliana was not studied using EST data.

TSS

Arabidopsis thaliana was not studied using FANTOM5 data.

Lab

retro_atha_14 was not experimentally validated.

Homology

Retrocopy orthology:

Arabidopsis thaliana does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

---

Parental genes homology:

Parental genes homology involve 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G37150	1 retrocopy	retro_atha_14 ,