RetrogeneDB ID: retro_lper_12

Retrocopy location

• Organism: Leersia perrieri
• Coordinates: 11:11256052..11258353(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: LPERR11G10560
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: LPERR10G13130
• Aliases: None
• Description: None

Sequence

>retro_lper_12
ATGAGGGGCGCCGTGGCGGTGGCAATCGCGGCGGCGATCGGCAACCTGCTGCAGGGATGGGACAACGCGACGATCGCCGG
CGCGGTGCTCTACATCAAGCGAGAATTCCACCTCGAATCCCAGCCCGCAATCGAGGGCCTCGTCGTGGCGGCCTCCCTCA
TCGGCGCGACGATCATCACCACCTTCTCCGGGCCGGCCTCCGACGCCGTGGGCCGGCGGCCGCTGCTGATCGCATCCTCC
CTCCTCTACCTCGCCGGCGGCCTCATCATGCTCTGGTCCCCATCCGTCTCCGTCCTCCTCCTCGCCCGCCTCGTCGACGG
CTTCGGCGTCGGCCTCGCCGTCACGCTCGTCCCCGTCTACATCTCCGAGACCTCGCCGCCGGAGATTCGGGGGCGGCTCA
ACACGCTGCCGCAGTTCACCGGGTCGGGAGGGATGTTCCTCTCCTACGTCATGATCTTCGCCATGACGGTCTCGTCTCCT
TCGCCCAATTGGCGTGCGATGCTTGGCGTGCTGTTTGTTCCGGCCGTGGCGTATCTGGTCGTGACGGTGTTCTTCCTGCC
GGAGTCGCCGCGGTGGCTGGTGAGCAAGGGGAGGATGAAGGAGGCAAGGGATGTGCTTGAGATGCTTCGTGGGAGAGACG
ATGTCTCCGGCGAGATGGCGTTGCTTGTCGAGGGGCTCGGCACCGGCGATGACACGCGGATCGAGGATTATGTCGTTGGG
CCGTCCGATGTCGGCGGCGACGGCGGTGGGGAGAATGAGAGGGATGATCAGACGGTGACGCTGTATGGGCCGGAGCAGGG
GCTTTCGTGGGTGGCGCAGCCGGTGGCGGGAGGAAGGGGATCGATGCTTGGGAGCGCATTGGCGTTGGGGATGCAGCCTT
CGTCGGGTTCGTGGCATGGGAGTATGTATGAGCAGATGAAGGATCCTGTGGTGGCGTTGCTCGGAAGTGTTCATGAGCGG
CTGCCGGCAGCGGAGAACGGCGGTGGGAGTATGAGGGGGAGCACGTTGTTCCCTAATTTGGGGAGTATGCTTAGTGTCGC
CGAGAGACCGGGCGGCGGCGGAGAAGGGTGGGATGAGGAGAATGTGCGGTCGGACACCGGTGATGATGAGGAGATGGAGG
ATGAGGAGGAGTATTTGTCTGGGAACGGGGATGCAGAAGCGGGATTGCAAGCGCCGCTGCTGTCACGGCAGAGCACGGAC
GTGGAGGTGAGTAGTGAGATACAGCCGGCGAGCCAGATGTCGATGCGGCGACATAGTAGCATCGGCGGCGGTGGGGTGGA
GGCGGCGAGCACGATGGGGATCGGAGGAGGGTGGCAGCTGGCATGGAAGTGGACGGAGAAGGTTGGCGCCGACGGCGTGA
AGCGTGGGGCCGTGAAGAGAATGTACCTGCACGAGGAGGGCGAGGTCACACCTGCCGCCATCGGCGGCGACGGAGGGGAC
ACGGCGGCGACGCCGTATGTGCACGCGGCGGCGTTGGTGAGCCGGTCGATGCTCTACACCAAGGACGTCCTGATCGGTCA
GAGCCCGACCGAGCCGGCGTTCGCGAACCCGCCCGAGGCGGTGGCGGCCGCGGCATCGGCCGGACACCCGGTCTGGCGTG
AGCTGCTTGAGCCCGGCGTCCGCCATGCGCTCTTCTGTGGTGTTACCATCCAGCTTCTACAACAGTTTTCTGGTATTAAT
GGTGTTCTCTACTACACTCCTCAAATACTTGACCAGGCTGGGGTTAGCGTTCTGCTTGCCAGCCTCGGCCTCAGCGCCGA
CTCGACCTCCATCCTCATCAGCGGCCTCACCACGCTCCTCATGCTCCCCTCTATCGGCGTCGCAATGCGTCTCATGGACG
TGTCGGGACGCCGGAAGTTGTTGCTGTGGACACTACCGGTGTTGATCCTTTCGCTGGTGGTGCTCGTGGTGGCGAACGTC
GTCCCCATGGCGGCGAAGGCGCACGCCGCGCTGTCGACGGGGAGCGTCATCGTCTACTTCTGCTGCTTCGTCATGGGGTT
TGGGCCGATCCCCAACATTCTCTGCGCCGAGATCTTCCCGACCAGGGTGAGGGGACTCTGCATCGCCATCTGCTCGCTCA
CGTTCTGGCTCGGCGACATCATTGTCACGTACAGCCTCCCCGTCATGCTCAGCTCCGTCGGGCTCGCCGGCGTCTTCGCC
TTCTACGCCGTAGTCTGCTGCGTGGCTCTCGTGTTCGTCGCGCTCAAGGTGCCTGAGACCAAGGGGTTGCCGCTCGAGGT
CATCATTGAGTTCTTCAACGTCGGCGCAAAGGCTGGCACTTTGCCTGAGGATGAGTATTAG

Alignment

ORF - retro_lper_12 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.45 %
• Parental protein coverage: 56.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGSMRSTLFPNFGSMFSVAEQQQAKADWDAESQREGDDYGSDHGGDDIEDSLQSPLISRQATSMEGKEIA
          .GSM.S......G......E........D.E.......Y.S..G..D.E..LQ.PL.SRQ.T..E.....
Retrocopy LGSMLSVAERPGGGGEGWDEENVRSDTGDDEEMEDEEEYLSGNG--DAEAGLQAPLLSRQSTDVEVSSEI

Parental  APHGSIMGAVGRGSGLMQGG-EAVSSMGIGGGWQLAWKWTEREGADGEKEGGFQRIYLHEEGVTGDRRGS
          .P.........R.S....GG.EA.S.MGIGGGWQLAWKWTE..GADG.K.G...R.YLHEE...G.....
Retrocopy QPASQM--SMRRHSSIGGGGVEAASTMGIGGGWQLAWKWTEKVGADGVKRGAVKRMYLHEE---GEVTPA

Parental  ILSLPGGDVPPGGEFVQAAALVSQPALYSKE-LMEQRLAGPAMVHPSE----AVSKG-PKWADLFEPGVK
          .....GGD.......V.AAALVS...LY.K..L..Q....PA...P.E....A.S.G.P.W..L.EPGV.
Retrocopy AIGGDGGDTA-ATPYVHAAALVSRSMLYTKDVLIGQSPTEPAFANPPEAVAAAASAGHPVWRELLEPGVR

Parental  HALFVGIGIQILQQFAGINGVLYYTPQILEQAGVGVLLSNIGLSSSSASILISGLTTLLMLPSIGIAMRL
          HALF.G..IQ.LQQF.GINGVLYYTPQIL.QAGV.VLL...GLS..S.SILISGLTTLLMLPSIG.AMRL
Retrocopy HALFCGVTIQLLQQFSGINGVLYYTPQILDQAGVSVLLASLGLSADSTSILISGLTTLLMLPSIGVAMRL

Parental  MDMSGRRFLLLATIPILIVALAILVLVNVVNVGTMVHASLSTISVILYFCFFVMGFGPIPNILCAEIFPT
          MD.SGRR.LLL.T.P.LI..L..LV..NVV......HA.LST.SVI.YFC.FVMGFGPIPNILCAEIFPT
Retrocopy MDVSGRRKLLLWTLPVLILSLVVLVVANVVPMAAKAHAALSTGSVIVYFCCFVMGFGPIPNILCAEIFPT

Parental  TVRGICIAICALTFWIGDIIVTYTLPVMLNAIGLAGVFGIYAVVCMIAFLFVFMKVPETKGMPLEVITEF
          .VRG.CIAIC.LTFW.GDIIVTY.LPVML...GLAGVF..YAVVC..A..FV..KVPETKG.PLEVI.EF
Retrocopy RVRGLCIAICSLTFWLGDIIVTYSLPVMLSSVGLAGVFAFYAVVCCVALVFVALKVPETKGLPLEVIIEF

Parental  FSVGAK
          F.VGAK
Retrocopy FNVGAK

Legend:

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

Expression

RNA-Seq

Leersia perrieri was not studied using RNA-Seq expression data.

ChIP-Seq

Leersia perrieri was not studied using ChIP-Seq data.

EST

Leersia perrieri was not studied using EST data.

TSS

Leersia perrieri was not studied using FANTOM5 data.

Lab

retro_lper_12 was not experimentally validated.

Homology

Retrocopy orthology:

Leersia perrieri 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.

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Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA033375	1 retrocopy	retro_oind_5,
Leersia perrieri	LPERR10G13130	1 retrocopy	retro_lper_12 ,