RetrogeneDB ID: retro_cpor_431

Retrocopy location

• Organism: Guinea Pig (Cavia porcellus)
• Coordinates: scaffold_15:2499326..2500120(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCPOG00000020389
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: AEBP2
• Ensembl ID: ENSCPOG00000007440
• Aliases: None
• Description: None

Sequence

>retro_cpor_431
ACAGCAGTTTCCAGTGGGCGTTCAACTCCAGGCATGATGAATGCACAAGGAAGCACTTCTTCAAGCAAAAATATTGCCTA
TAATTGTTGCTGGGACCAGTGCCAGGCTTGCTTCAGCTCTAGCCAGATCTGGCAGATCACATCGTTCCATACGTGTAGAT
GGTCAGCGAGGAGGGCGTCTGTTTGCTTATGGAAAGGCTGTGAAGTGTGTAACACTCCCGCTCCCAGTCGGGGTTGGTCA
CAGACACACGCCGCCGCACGGGGGAGACAAGCCCTGCAAGCTGCTGTTGGTGGCTGCAGCGCCAGCTTTGTCTCAGGGAG
CACTAGCTCGCCACGTACCCACGCACTGCAGGCCGCAGAACTCCGCAAAGGTTCCAGCCAGCCAAAGGCCAAAGCAGAAT
CTCCTTCTAAAGCTGGAATAAACAAAAGGAGGAAGTTAAGGAACAAAAGACACGCTCGTTACCACGACCGCGTGACTTCT
TGGATGCACAAACACTGGATGCGATAAGACATCGAGCCACATGCTTTAACCTCAGCGCATATAGAAAGTTTAGGGAAGGA
CACAGTGTTGTTTTTCATAGTATTGTAATAGCTAAGAGAAAAGAGGATTCTGGGAAGATAAAACTTTTGCTACACTGGAT
GCCTGAAGACGTTCTGCCAGATGTGTGGGTGAATGAGAGTGAACGACATCAACTAAAAACTAAAGTAGTTCAGTTATCAA
AGCTGCCCAAAGATACTGCGTTGCTTTTGGACCCAAACATATACAGAGCAATGCCGCCGAAGAGGTTGAAGAGA

Alignment

ORF - retro_cpor_431 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.18 %
• Parental protein coverage: 62.94 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  STISSGRSTPAMMNGQGSTTSSSKNIAYNCCWDQCQACFNSS-PDLADHI-RSIHVDGQRGG-VFVCLWK
          ...SSGRSTP.MMN.QGS.TSSSKNIAYNCCWDQCQACF.SS.PDLADHI.RSI.VDGQRGG...VCLWK
Retrocopy TAVSSGRSTPGMMNAQGS-TSSSKNIAYNCCWDQCQACFSSS<PDLADHI<RSIRVDGQRGG<ASVCLWK

Parental  GCKVYNTPSTSQSWLQRHMLTHSGDKPFKCVVGGCNASFASQGGLARHVPTHFSQ-QNSSKVSSQPKAKE
          GC.V.NTP..S..W.Q.H.....G.......VGGC.ASF.S..G......TH..Q.....K.SSQPKAK.
Retrocopy GCEVCNTPAPSRGWSQTHAAAR-GRQALQAAVGGCSASFVS--GSTSSPRTHALQAAELRKGSSQPKAKA

Parental  ESPSKAGMNKRRKLKNKRR-RSLPRPHDFFDAQTLDAIRHRAICFNLSAHIESLGKGHSVVFHSTVIAKR
          ESPSKAG.NKRRKL.NKR..RSLPRP.DF.DAQTLDAIRHRA.CFNLSA.......GHSVVFHS.VIAKR
Retrocopy ESPSKAGINKRRKLRNKRH<RSLPRPRDFLDAQTLDAIRHRATCFNLSAY-RKFREGHSVVFHSIVIAKR

Parental  KEDSGKIKLLLHWMPEDILPDVWVNESERHQLKTKVVHLSKLPKDTALLLDPNIYRTMPQKRLKR
          KEDSGKIKLLLHWMPED.LPDVWVNESERHQLKTKVV.LSKLPKDTALLLDPNIYR.MP.KRLKR
Retrocopy KEDSGKIKLLLHWMPEDVLPDVWVNESERHQLKTKVVQLSKLPKDTALLLDPNIYRAMPPKRLKR

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	10.24 RPM
SRP017611_kidney	0.00 RPM	16.54 RPM
SRP017611_liver	0.09 RPM	10.58 RPM
SRP040447_lung	0.00 RPM	17.10 RPM
SRP040447_skeletal_muscle	0.00 RPM	6.97 RPM

ChIP-Seq

Cavia porcellus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cpor_431 retrocopy.

TSS

Cavia porcellus was not studied using FANTOM5 data.

Lab

retro_cpor_431 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000007440	1 retrocopy	retro_cpor_431 ,
Myotis lucifugus	ENSMLUG00000006293	1 retrocopy	retro_mluc_1637,
Oryctolagus cuniculus	ENSOCUG00000016677	2 retrocopies	retro_ocun_1207, retro_ocun_1672,
Rattus norvegicus	ENSRNOG00000008929	1 retrocopy	retro_rnor_875,