RetrogeneDB ID: retro_ecab_1069

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:53339629..53340283(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLEKHB2
• Ensembl ID: ENSECAG00000017331
• Aliases: None
• Description: pleckstrin homology domain containing, family B (evectins) member 2 [Source:HGNC Symbol;Acc:19236]

Sequence

>retro_ecab_1069
GTGAAGAGTGGGTGGTTGCTGCGACAGAGCAGTATTTGGAAGCGCTGGAAGAAATAGTTTGGCCTGTGGTCAGATGGTCA
CCTGATCTATTAGGATGACCAAACTCGGCAGAGTGTCGAGGATAAGGTCCACATGCTGGTGGACTGCATCAATATCTGCA
CAGGGCGTGAATGCCAGGATGTGCAGCCTCCAGATGGGAAGCCGAAAGACTGTATGCTGCAGATTCTTCGCCGAGATGGG
CGAACTATCAGTCTTTGTTCAGAAAGCACAGAAGATTGTTTGGCCCAGAAATTTATGCTTCAGGATTCCAGGATAAATAC
GGCTTATGTTGGCTTAGAAGTCAGGTATGATGAGATGGCTGTCGCTTCTTCCCCACCTCCTTACACAGCCTATGCTGCAC
CGACCCCTGAGCAGACATATGGCTATGGTCCATACGGTGGTGCATAGCCGCCAGGAACTCAAGTTGTCCATGCTGCGAAT
AGGCAGGCTTATGCTGCACCCTACCAGTACCCACATGCAGGACTTTATGGACACCAGCCTGCCAACCAGGTCATCATTTG
TGAGCGATATGGAGACAATGACAGTGATCTGACACTGGGCATGCTGGCTGGAGCAGCCACAGGCATGGCCTTAGGGTCTC
TGTTCTGGGTCTTC

Alignment

ORF - retro_ecab_1069 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.65 %
• Parental protein coverage: 98.65 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VKSGWLLRQSTILKRWKKNWFDLWSDGHLIYYDDQTRQSVEDKVHMPVDCINIRMGHECRDVQPPDGKPK
          VKSGWLLRQS.I.KRWKK..F.LWSDGHLIY.DDQTRQSVEDKVHM.VDCINI..G.EC.DVQPPDGKPK
Retrocopy VKSGWLLRQSSIWKRWKK*-FGLWSDGHLIY*DDQTRQSVEDKVHMLVDCINICTGRECQDVQPPDGKPK

Parental  DCMLQIVCRDGKTISLCAESTDDCLAWKFTLQDSRTNTAYVGSEVMYDETAVAASPPPYTAYATPTPEQA
          DCMLQI..RDG.TISLC.EST.DCLA.KF.LQDSR.NTAYVG.EV.YDE.AVA.SPPPYTAYA.PTPEQ.
Retrocopy DCMLQILRRDGRTISLCSESTEDCLAQKFMLQDSRINTAYVGLEVRYDEMAVASSPPPYTAYAAPTPEQT

Parental  YGYGPYSGVYPPGTQVVYTANGQAYAVPYQYPCAGLYGQQPANQVIIRERYRDNDTDLALGMLAGAATGM
          YGYGPY.G..PPGTQVV..AN.QAYA.PYQYP.AGLYG.QPANQVII.ERY.DND.DL.LGMLAGAATGM
Retrocopy YGYGPYGGA*PPGTQVVHAANRQAYAAPYQYPHAGLYGHQPANQVIICERYGDNDSDLTLGMLAGAATGM

Parental  ALGSLFWVF
          ALGSLFWVF
Retrocopy ALGSLFWVF

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
SRP021940_articular_cartilage	0.00 RPM	16.53 RPM
SRP021940_cerebellum	0.00 RPM	103.19 RPM
SRP021940_embryo	0.00 RPM	17.06 RPM
SRP021940_placental_villous	0.00 RPM	28.91 RPM
SRP021940_synovial_membrane	0.00 RPM	30.25 RPM
SRP021940_testis	0.00 RPM	56.91 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1069 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1069 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1069 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,