RetrogeneDB ID: retro_btau_1635

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:11064114..11064777(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000034560
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSBTAG00000000941
• Aliases: None
• Description: pleckstrin homology domain-containing family B member 2 [Source:RefSeq peptide;Acc:NP_001076998]

Sequence

>retro_btau_1635
ATGGCATTTGTGAAGAGTGGATGGTTGCTGCGACAGAGTACTATTTTGAAGCGCTGGAAGAAGAATTGGTTTGACCTGTG
GTCAGATGGTCACCTGATCTATTATGATGACCAGACTCGGCAGAGTGTAGAAGATAAGGTCCCCATGCCAGTGGGCTGCA
TCAACATTCGCATGGGGCATGAGTGTCGGGATATTCAACCACCAGATGGGAAGCCAAAAGACCGTATGCTGCAGGTTGTT
TGCCGAGATGGAAAAACCATCAGTCTTTGTGCAGAAAGCACAGATGATTGTTTGGCCTGGAAGTTTACACTCCAGGATTC
CAGGACAAACACAGCTTATGTTGGCTCAGAAGTCATGTATGATGAGACAGCTGTGGCTTCCTCCCCACCTCCTTACACAG
CGTATGCTGCACCGACCCCTGAGGCATATGGCTATGGTCCATACAGTGGTGCATACCCACCAGGAACTCAAGTTGTCTAT
GCTGCAAATGGACAGGCTTATGCTGTACCCTATCAGTACCCGTATGCTGGGCTTTATGGACAGCAGCCTGCCAACCAAGT
CATCATTCGTGAGCGGCACCGAGACAACAACAGCGACCTGGCGCTGGGCATGCTGGCCGGAGCAGCCACAGGCATGGCCC
TGGCGTCTCTGTTCTGGGTCTTC

Alignment

ORF - retro_btau_1635 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAFVKSGWLLRQSTILKRWKKNWFDLWSDGHLIYYDAQTRQSVEDKVHMPVDCINIRMGRECRDIQPPDG
          MAFVKSGWLLRQSTILKRWKKNWFDLWSDGHLIYYD.QTRQSVEDKV.MPV.CINIRMG.ECRDIQPPDG
Retrocopy MAFVKSGWLLRQSTILKRWKKNWFDLWSDGHLIYYDDQTRQSVEDKVPMPVGCINIRMGHECRDIQPPDG

Parental  KPKDCMLQIVCRDGKTISLCAESTDDCLAWKFTLQDSRTNTAYVGSEVMYDETAVASSPPPYTAYAAPTP
          KPKD.MLQ.VCRDGKTISLCAESTDDCLAWKFTLQDSRTNTAYVGSEVMYDETAVASSPPPYTAYAAPTP
Retrocopy KPKDRMLQVVCRDGKTISLCAESTDDCLAWKFTLQDSRTNTAYVGSEVMYDETAVASSPPPYTAYAAPTP

Parental  EQAYGYGPYSGAYPPGTQVVYAANGQAYAVPYQYPYAGLYGQQPANQVIIRERYRDNDSDLALGMLAGAA
          E.AYGYGPYSGAYPPGTQVVYAANGQAYAVPYQYPYAGLYGQQPANQVIIRER.RDN.SDLALGMLAGAA
Retrocopy E-AYGYGPYSGAYPPGTQVVYAANGQAYAVPYQYPYAGLYGQQPANQVIIRERHRDNNSDLALGMLAGAA

Parental  TGMALGSLFWVF
          TGMAL.SLFWVF
Retrocopy TGMALASLFWVF

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
ERP005899_liver	0.07 RPM	18.53 RPM
ERP005899_muscle	0.63 RPM	109.91 RPM
SRP017611_brain	0.69 RPM	198.57 RPM
SRP017611_kidney	0.53 RPM	152.21 RPM
SRP017611_liver	0.08 RPM	9.51 RPM
SRP030211_testis	0.15 RPM	90.33 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1635 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1635 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1635 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000000941	2 retrocopies	retro_btau_1134, retro_btau_1635 ,
Cavia porcellus	ENSCPOG00000026329	1 retrocopy	retro_cpor_985,
Equus caballus	ENSECAG00000017331	1 retrocopy	retro_ecab_1069,
Felis catus	ENSFCAG00000027063	1 retrocopy	retro_fcat_213,
Homo sapiens	ENSG00000115762	1 retrocopy	retro_hsap_1890,
Meleagris gallopavo	ENSMGAG00000001052	1 retrocopy	retro_mgal_17,
Monodelphis domestica	ENSMODG00000018634	1 retrocopy	retro_mdom_720,
Nomascus leucogenys	ENSNLEG00000010698	2 retrocopies	retro_nleu_1471, retro_nleu_2016,
Oryctolagus cuniculus	ENSOCUG00000024282	1 retrocopy	retro_ocun_654,
Otolemur garnettii	ENSOGAG00000028408	2 retrocopies	retro_ogar_2771, retro_ogar_703,
Pongo abelii	ENSPPYG00000012740	1 retrocopy	retro_pabe_1570,
Ictidomys tridecemlineatus	ENSSTOG00000020509	1 retrocopy	retro_itri_56,