RetrogeneDB ID: retro_cpor_896

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_32:17663573..17664701(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: BLMH
• Ensembl ID: ENSCPOG00000005048
• Aliases: None
• Description: None

Sequence

>retro_cpor_896
ACGAGACTGAATTTGGAGAAGGTGGCTGCTCTGACCCAGAAACTGAACTCCAGCCCTCAGTTTGTACTCCCCAGAATGCT
GGAACCATCCACAACCCTCTGGACCTCCATCTGAAAAGAGCCATGGTACAGGACACCCATGTATTCCTACACGCTGTGCC
TCAGAAAGGCAAGCCAGTCACCAGCCAGAGGAGCTCCAGATGATGCTGGGTCTTTTCTTGTCTGAATGTTATGAGACTTC
CATTCATGAAAAAGTTAAATATTCAAGATTTTGAGTTTAGTCAATCTCGCCTCTTTTGGGGTGGACTGGGTCAAATGCTA
TTATTTTTCCTTCAATGCTTTGTAGACACAGCCCAGAAAAAGGAGCTTTAGGATGGGAGGCTGGTGTAGTGTTTGCTTGT
GAATCCTACAAATGATGGTGGGCAGTAGGATATGCTTGCCAATATTATGTTTAAATATGGTGTTGTCCCTAATAAATGCT
TCCCTGAATCTCATATAACAGAGGCCAATGAGAAGGGTAAGTCATATTCTGAAACACAGCATAAGAGAATTCTGTATACA
AATACAGAACTTGGTACAACATGGAACTCCCAAAAGAGAAAGCCCTGCTACAAAGGATGCCATGATGGATGAGATATTCT
GAGTGGTGTCATCTGTTTGGGTAATCCTCCAGAGACACTTGACTGGCATTATCATGACAAGATAAAAATTATCACAAGAC
CGGCCCTATAACACCTTGAGGTTTTACAGGGAACACGCCAAGCTTCTCCTCAGTATGGAAGATAAGATTGGTTTTATGAT
TCATCCATGGCCCCAGCACATGGAAAACAAACCTTATCCTGTAGACTCCTTGACAATGCGGTTGGAAGGAAAAGATCTCC
GTTTAACAACCAATCCACTGACTTCTTGAAAAAGATGATCACCGCTCCCATCAAAGATGGAAAGGCTGTGTGGCTAGGCT
GTGGTGCTGGAAGACACTTCAGTGGCAAGCTGGGTCTCGGTGACACGGATGTCTGTGACTGTGAATTAATGTCTGATGTC
TCCTGAAGAACACGGACAAAACTGAGAAGCTGTCTTTTGGTGCGTCACCTATGATCACACTAGGACCTTCACTGCTGTCC
TGGAGAGG

Alignment

ORF - retro_cpor_896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.53 %
• Parental protein coverage: 82.39 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 8

Retrocopy - Parental Gene Alignment:

Parental  TGLDSEQVSAVIQKLKSDPQFVLA-QNVGTTHDLLDICLKRATVQCAQHVFQHVVPLEGKPVTNQKSSGR
          T.L..E.V.A..QKL.S.PQFVL..QN.GT.H..LD..LKRA.VQ...HVF.H.VP..GKPVT.Q.SS..
Retrocopy TRLNLEKVAALTQKLNSSPQFVLP<QNAGTIHNPLDLHLKRAMVQDT-HVFLHAVPQKGKPVTSQRSSR*

Parental  CWIFSCLNVMRLPFMKKLNIEEFEFSQSYLFFWDKVERCYFFLNAFVDTAQKKEPEDGRLVQYLLMNPTN
          CW.FSCLNVMRLPFMKKLNI..FEFSQS.LF.........FFL..FVDTAQKKE..DGRLV..LL.NPTN
Retrocopy CWVFSCLNVMRLPFMKKLNIQDFEFSQSRLFWGGLGQMLLFFLQCFVDTAQKKEL*DGRLV*CLLVNPTN

Parental  DGGQWDMLVNIVEKYGVVPKKCFPESHTTEAS-RRMNDILNHKMREFCIRLRNLVHSGATKGEISATQDV
          DGGQ.DML.NI..KYGVVP.KCFPESH.TEA..RR...IL.H..REFCI...NLV..G..K.E..AT.D.
Retrocopy DGGQ*DMLANIMFKYGVVPNKCFPESHITEAN>RRVSHILKHSIREFCIQIQNLVQHGTPKRESPATKDA

Parental  MMEEILRVV-CICLGNPPETFTWEYRDK-DKNYHKIGPITP-LEFYREHVKPLFNMEDKICFVNDPRPQH
          MM.EI..VV..ICLGNPPET..W.Y.DK.DKNYHK.GPITP.L.FYREH.K.L..MEDKI.F...P.PQH
Retrocopy MMDEIF*VV<VICLGNPPETLDWHYHDK<DKNYHKTGPITP<LRFYREHAKLLLSMEDKIGFMIHPWPQH

Parental  KYNKLYTVD-YLSNMVGGRKTLYNNQPIDFLKKMVAASIKDGEAVWFGCDVGKHFNGKLGLSDMNIYDHE
          ..NK.Y.VD..L.N.VG......NNQ..DFLKKM..A.IKDG.AVW.GC..G.HF.GKLGL.D....D.E
Retrocopy MENKPYPVD<LLDNAVGRKRSPFNNQSTDFLKKMITAPIKDGKAVWLGCGAGRHFSGKLGLGDTDVCDCE

Parental  LVFGVS-LKNMNKAERLSFGESLM-THAMTFTAFSEK
          L...VS.LKN..K.E.LSFG.S.M..H..TFTA..E.
Retrocopy LMSDVS<LKNTDKTEKLSFGASPM<DHTRTFTAVLER

Legend:

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

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP017611_brain	0.00 RPM	22.66 RPM
SRP017611_kidney	0.10 RPM	30.36 RPM
SRP017611_liver	0.00 RPM	33.78 RPM
SRP040447_lung	0.03 RPM	35.28 RPM
SRP040447_skeletal_muscle	0.00 RPM	45.59 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_896 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_896 was not experimentally validated.

Homology

Retrocopy orthology:

Cavia porcellus 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000021370	1 retrocopy	retro_btau_1510,
Callithrix jacchus	ENSCJAG00000013781	1 retrocopy	retro_cjac_2998,
Cavia porcellus	ENSCPOG00000005048	1 retrocopy	retro_cpor_896 ,
Macropus eugenii	ENSMEUG00000008938	1 retrocopy	retro_meug_2120,
Rattus norvegicus	ENSRNOG00000003563	1 retrocopy	retro_rnor_566,
Tursiops truncatus	ENSTTRG00000016341	1 retrocopy	retro_ttru_1915,
Vicugna pacos	ENSVPAG00000003571	1 retrocopy	retro_vpac_74,